Perović, Vladimir R.

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Authority KeyName Variants
orcid::0000-0002-3700-6452
  • Perović, Vladimir R. (39)
Projects
Application of the EIIP/ISM bioinformatics platform in discovery of novel therapeutic targets and potential therapeutic molecules An integral study to identify the regional genetic and environmental risk factors for the common noncommunicable diseases in the human population of Serbia - INGEMA_S
BBSRC (BB/K000446/1) COST Action (BM1405)
Estonian Ministry for Education and Research [IUT34-14], EU COST Action [CM1307] European Commission [TRIoH LSHG-CT-2003-503480]
H2020-MSCA-RISE project REFRACT [GA No. 823886] TRANSPLANT - Trans-national Infrastructure for Plant Genomic Science
MAESTRA - Learning from Massive, Incompletely annotated, and Structured Data Synthesis, Quantitative Structure and Activity Relationship, Physico-Chemical Characterisation and Analysis of Pharmacologically Active Substances
Interraction of etiopathogenetic mechanisms of periodontal disease and periimplantitis with the systemic disorders of the present day Pharmacodynamic and pharmacogenomic research of new drugs in the treatment of solid tumors
Multimodal Biometry in Identity Management Italian National Research Programme on AIDS 40H26
Ministry of Foreign Affairs, Luxembourg Ministry of Science and Technological Development of the Republic of Serbia [143001]
Ministry of Science and Technological Development of the Republic of Serbia [143001], COST Action [B28] Ministry of Science of the Republic of Serbia [143001]
MRC Institute of Hearing Research Early Career Award National Institute of Allergy and Infectious Diseases [Research Grant 1R01AI12123701]
National Science Foundation [DBI-1458477, DBI-1458443, DBI-1458390, DBI-1458359, IIS-1319551, DBI-1262189, DBI-1149224], National Institutes of Health [R01GM093123, R01GM097528, R01GM076990, R01GM071749, R01LM009722, UL1TR000423], National Natural Science Foundation of China [3147124, 91231116], National Basic Research Program of China [2012CB316505], NSERC [RGPIN 371348-11], Microsoft Research/FAPESP grant [2009/53161-6], FAPESP [2010/50491-1], Biotechnology and Biological Sciences Research Council [BB/L020505/1, BB/F020481/1, BB/K004131/1, BB/F00964X/1, BB/L018241/1], Spanish Ministry of Economics and Competitiveness [BIO2012-40205], KU Leuven [CoE PFV/10/016 SymBioSys], Newton International Fellowship Scheme of the Royal Society grant [NF080750], Gordon and Betty Moore Foundations Data-Driven Discovery Initiative grant [GBMF4552], Academy of Finland, British Heart Foundation [RG/13/5/30112], Parkinsons UK [G-1307], Alexander von Humboldt Foundation through the German Federal Ministry for Education and Research, Ernst Ludwig Ehrlich Studienwerk, U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research grant [DE-AC02-05CH11231], Australian Research Council grant [DP150101550], NIH [T15 LM00945102], FP7 REGPOT grant InnoMol, University of Padova [CPDA138081/13, GRIC13AAI9], Swiss National Science Foundation [150654], UK BBSRC grant [BB/M015009/1], ICREA University of Parma, Italy, Turku University Hospital, Finland, Chiesi Foundation

Author's Bibliography

Alignment-free method for functional annotation of amino acid substitutions: Application on epigenetic factors involved in hematologic malignancies

Gemović, Branislava S.; Perović, Vladimir R.; Davidović, Radoslav S.; Drljača, Tamara; Veljković, Nevena V.

(2021)

TY  - JOUR
AU  - Gemović, Branislava S.
AU  - Perović, Vladimir R.
AU  - Davidović, Radoslav S.
AU  - Drljača, Tamara
AU  - Veljković, Nevena V.
PY  - 2021
UR  - https://vinar.vin.bg.ac.rs/handle/123456789/8894
AB  - For the last couple of decades, there has been a significant growth in sequencing data, leading to an extraordinary increase in the number of gene variants. This places a challenge on the bioinformatics research community to develop and improve computational tools for functional annotation of new variants. Genes coding for epigenetic regulators have important roles in cancer pathogenesis and mutations in these genes show great potential as clinical biomarkers, especially in hematologic malignancies. Therefore, we developed a model that specifically focuses on these genes, with an assumption that it would outperform general models in predicting the functional effects of amino acid substitutions. EpiMut is a standalone software that implements a sequence based alignment-free method. We applied a two-step approach for generating sequence based features, relying on the biophysical and biochemical indices of amino acids and the Fourier Transform as a sequence transformation method. For each gene in the dataset, the machine learning algorithm–Naïve Bayes was used for building a model for prediction of the neutral or disease-related status of variants. EpiMut outperformed state-of-the-art tools used for comparison, PolyPhen-2, SIFT and SNAP2. Additionally, EpiMut showed the highest performance on the subset of variants positioned outside conserved functional domains of analysed proteins, which represents an important group of cancer-related variants. These results imply that EpiMut can be applied as a first choice tool in research of the impact of gene variants in epigenetic regulators, especially in the light of the biomarker role in hematologic malignancies. EpiMut is freely available at https://www.vin.bg.ac.rs/180/tools/epimut.php.
T2  - PLOS One
T1  - Alignment-free method for functional annotation of amino acid substitutions: Application on epigenetic factors involved in hematologic malignancies
VL  - 16
IS  - 1
SP  - e0244948
DO  - 10.1371/journal.pone.0244948
ER  - 
@article{
author = "Gemović, Branislava S. and Perović, Vladimir R. and Davidović, Radoslav S. and Drljača, Tamara and Veljković, Nevena V.",
year = "2021",
url = "https://vinar.vin.bg.ac.rs/handle/123456789/8894",
abstract = "For the last couple of decades, there has been a significant growth in sequencing data, leading to an extraordinary increase in the number of gene variants. This places a challenge on the bioinformatics research community to develop and improve computational tools for functional annotation of new variants. Genes coding for epigenetic regulators have important roles in cancer pathogenesis and mutations in these genes show great potential as clinical biomarkers, especially in hematologic malignancies. Therefore, we developed a model that specifically focuses on these genes, with an assumption that it would outperform general models in predicting the functional effects of amino acid substitutions. EpiMut is a standalone software that implements a sequence based alignment-free method. We applied a two-step approach for generating sequence based features, relying on the biophysical and biochemical indices of amino acids and the Fourier Transform as a sequence transformation method. For each gene in the dataset, the machine learning algorithm–Naïve Bayes was used for building a model for prediction of the neutral or disease-related status of variants. EpiMut outperformed state-of-the-art tools used for comparison, PolyPhen-2, SIFT and SNAP2. Additionally, EpiMut showed the highest performance on the subset of variants positioned outside conserved functional domains of analysed proteins, which represents an important group of cancer-related variants. These results imply that EpiMut can be applied as a first choice tool in research of the impact of gene variants in epigenetic regulators, especially in the light of the biomarker role in hematologic malignancies. EpiMut is freely available at https://www.vin.bg.ac.rs/180/tools/epimut.php.",
journal = "PLOS One",
title = "Alignment-free method for functional annotation of amino acid substitutions: Application on epigenetic factors involved in hematologic malignancies",
volume = "16",
number = "1",
pages = "e0244948",
doi = "10.1371/journal.pone.0244948"
}
Gemović, B. S., Perović, V. R., Davidović, R. S., Drljača, T.,& Veljković, N. V. (2021). Alignment-free method for functional annotation of amino acid substitutions: Application on epigenetic factors involved in hematologic malignancies.
PLOS One, 16(1), e0244948.
https://doi.org/10.1371/journal.pone.0244948
Gemović BS, Perović VR, Davidović RS, Drljača T, Veljković NV. Alignment-free method for functional annotation of amino acid substitutions: Application on epigenetic factors involved in hematologic malignancies. PLOS One. 2021;16(1):e0244948
Gemović Branislava S., Perović Vladimir R., Davidović Radoslav S., Drljača Tamara, Veljković Nevena V., "Alignment-free method for functional annotation of amino acid substitutions: Application on epigenetic factors involved in hematologic malignancies" PLOS One, 16, no. 1 (2021):e0244948,
https://doi.org/10.1371/journal.pone.0244948 .
1

Tally-2.0: upgraded validator of tandem repeat detection in protein sequences

Perović, Vladimir R.; Leclercq, Jeremy Y; Šumonja, Neven; Richard, Francois D; Veljković, Nevena V.; Kajava, Andrey V.

(2020)

TY  - JOUR
AU  - Perović, Vladimir R.
AU  - Leclercq, Jeremy Y
AU  - Šumonja, Neven
AU  - Richard, Francois D
AU  - Veljković, Nevena V.
AU  - Kajava, Andrey V.
PY  - 2020
UR  - https://vinar.vin.bg.ac.rs/handle/123456789/8997
AB  - Motivation: Proteins containing tandem repeats (TRs) are abundant, frequently fold in elongated non-globular structures and perform vital functions. A number of computational tools have been developed to detect TRs in protein sequences. A blurred boundary between imperfect TR motifs and non-repetitive sequences gave rise to necessity to validate the detected TRs. Results: Tally-2.0 is a scoring tool based on a machine learning (ML) approach, which allows to validate the results of TR detection. It was upgraded by using improved training datasets and additional ML features. Tally-2.0 performs at a level of 93% sensitivity, 83% specificity and an area under the receiver operating characteristic curve of 95%.
T2  - Bioinformatics
T1  - Tally-2.0: upgraded validator of tandem repeat detection in protein sequences
VL  - 36
IS  - 10
SP  - 3260
EP  - 3262
DO  - 10.1093/bioinformatics/btaa121
ER  - 
@article{
author = "Perović, Vladimir R. and Leclercq, Jeremy Y and Šumonja, Neven and Richard, Francois D and Veljković, Nevena V. and Kajava, Andrey V.",
year = "2020",
url = "https://vinar.vin.bg.ac.rs/handle/123456789/8997",
abstract = "Motivation: Proteins containing tandem repeats (TRs) are abundant, frequently fold in elongated non-globular structures and perform vital functions. A number of computational tools have been developed to detect TRs in protein sequences. A blurred boundary between imperfect TR motifs and non-repetitive sequences gave rise to necessity to validate the detected TRs. Results: Tally-2.0 is a scoring tool based on a machine learning (ML) approach, which allows to validate the results of TR detection. It was upgraded by using improved training datasets and additional ML features. Tally-2.0 performs at a level of 93% sensitivity, 83% specificity and an area under the receiver operating characteristic curve of 95%.",
journal = "Bioinformatics",
title = "Tally-2.0: upgraded validator of tandem repeat detection in protein sequences",
volume = "36",
number = "10",
pages = "3260-3262",
doi = "10.1093/bioinformatics/btaa121"
}
Perović, V. R., Leclercq, J. Y., Šumonja, N., Richard, F. D., Veljković, N. V.,& Kajava, A. V. (2020). Tally-2.0: upgraded validator of tandem repeat detection in protein sequences.
Bioinformatics, 36(10), 3260-3262.
https://doi.org/10.1093/bioinformatics/btaa121
Perović VR, Leclercq JY, Šumonja N, Richard FD, Veljković NV, Kajava AV. Tally-2.0: upgraded validator of tandem repeat detection in protein sequences. Bioinformatics. 2020;36(10):3260-3262
Perović Vladimir R., Leclercq Jeremy Y, Šumonja Neven, Richard Francois D, Veljković Nevena V., Kajava Andrey V., "Tally-2.0: upgraded validator of tandem repeat detection in protein sequences" Bioinformatics, 36, no. 10 (2020):3260-3262,
https://doi.org/10.1093/bioinformatics/btaa121 .
2
1
1
1

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

Zhou, Naihui; Jiang, Yuxiang; Bergquist, Timothy R; Lee, Alexandra J; Kacsoh, Balint Z; Crocker, Alex W; Lewis, Kimberley A; Georghiou, George; Nguyen, Huy N; Hamid, Md Nafiz; Davis, Larry; Dogan, Tunca; Atalay, Volkan; Rifaioglu, Ahmet S; Dalkıran, Alperen; Cetin Atalay, Rengul; Zhang, Chengxin; Hurto, Rebecca L; Freddolino, Peter L; Zhang, Yang; Bhat, Prajwal; Supek, Fran; Fernández, José M; Gemović, Branislava S.; Perović, Vladimir R.; Davidović, Radoslav S.; Šumonja, Neven; Veljković, Nevena V.; Asgari, Ehsaneddin; Mofrad, Mohammad R.K.; Profiti, Giuseppe; Savojardo, Castrense; Martelli, Pier Luigi; Casadio, Rita; Boecker, Florian; Schoof, Heiko; Kahanda, Indika; Thurlby, Natalie; McHardy, Alice C; Renaux, Alexandre; Saidi, Rabie; Gough, Julian; Freitas, Alex A; Antczak, Magdalena; Fabris, Fabio; Wass, Mark N; Hou, Jie; Cheng, Jianlin; Wang, Zheng; Romero, Alfonso E; Paccanaro, Alberto; Yang, Haixuan; Goldberg, Tatyana; Zhao, Chenguang; Holm, Liisa; Törönen, Petri; Medlar, Alan J; Zosa, Elaine; Borukhov, Itamar; Novikov, Ilya; Wilkins, Angela; Lichtarge, Olivier; Chi, Po-Han; Tseng, Wei-Cheng; Linial, Michal; Rose, Peter W; Dessimoz, Christophe; Vidulin, Vedrana; Dzeroski, Saso; Sillitoe, Ian; Das, Sayoni; Lees, Jonathan Gill; Jones, David T; Wan, Cen; Cozzetto, Domenico; Fa, Rui; Torres, Mateo; Warwick Vesztrocy, Alex; Rodriguez, Jose Manuel; Tress, Michael L; Frasca, Marco; Notaro, Marco; Grossi, Giuliano; Petrini, Alessandro; Re, Matteo; Valentini, Giorgio; Mesiti, Marco; Roche, Daniel B; Reeb, Jonas; Ritchie, David W; Aridhi, Sabeur; Alborzi, Seyed Ziaeddin; Devignes, Marie-Dominique; Koo, Da Chen Emily; Bonneau, Richard; Gligorijević, Vladimir; Barot, Meet; Fang, Hai; Toppo, Stefano; Lavezzo, Enrico; Falda, Marco; Berselli, Michele; Tosatto, Silvio C.E.; Carraro, Marco; Piovesan, Damiano; Ur Rehman, Hafeez; Mao, Qizhong; Zhang, Shanshan; Vucetic, Slobodan; Black, Gage S; Jo, Dane; Suh, Erica; Dayton, Jonathan B; Larsen, Dallas J; Omdahl, Ashton R; McGuffin, Liam J; Brackenridge, Danielle A; Babbitt, Patricia C; Yunes, Jeffrey M; Fontana, Paolo; Zhang, Feng; Zhu, Shanfeng; You, Ronghui; Zhang, Zihan; Dai, Suyang; Yao, Shuwei; Tian, Weidong; Cao, Renzhi; Chandler, Caleb; Amezola, Miguel; Johnson, Devon; Chang, Jia-Ming; Liao, Wen-Hung; Liu, Yi-Wei; Pascarelli, Stefano; Frank, Yotam; Hoehndorf, Robert; Kulmanov, Maxat; Boudellioua, Imane; Politano, Gianfranco; Di Carlo, Stefano; Benso, Alfredo; Hakala, Kai; Ginter, Filip; Mehryary, Farrokh; Kaewphan, Suwisa; Björne, Jari; Moen, Hans; Tolvanen, Martti E.E.; Salakoski, Tapio; Kihara, Daisuke; Jain, Aashish; Šmuc, Tomislav; Altenhoff, Adrian; Ben-Hur, Asa; Rost, Burkhard; Brenner, Steven E; Orengo, Christine A; Jeffery, Constance J; Bosco, Giovanni; Hogan, Deborah A; Martin, Maria J; O’Donovan, Claire; Mooney, Sean D; Greene, Casey S; Radivojac, Predrag; Friedberg, Iddo

(2019)

TY  - JOUR
AU  - Zhou, Naihui
AU  - Jiang, Yuxiang
AU  - Bergquist, Timothy R
AU  - Lee, Alexandra J
AU  - Kacsoh, Balint Z
AU  - Crocker, Alex W
AU  - Lewis, Kimberley A
AU  - Georghiou, George
AU  - Nguyen, Huy N
AU  - Hamid, Md Nafiz
AU  - Davis, Larry
AU  - Dogan, Tunca
AU  - Atalay, Volkan
AU  - Rifaioglu, Ahmet S
AU  - Dalkıran, Alperen
AU  - Cetin Atalay, Rengul
AU  - Zhang, Chengxin
AU  - Hurto, Rebecca L
AU  - Freddolino, Peter L
AU  - Zhang, Yang
AU  - Bhat, Prajwal
AU  - Supek, Fran
AU  - Fernández, José M
AU  - Gemović, Branislava S.
AU  - Perović, Vladimir R.
AU  - Davidović, Radoslav S.
AU  - Šumonja, Neven
AU  - Veljković, Nevena V.
AU  - Asgari, Ehsaneddin
AU  - Mofrad, Mohammad R.K.
AU  - Profiti, Giuseppe
AU  - Savojardo, Castrense
AU  - Martelli, Pier Luigi
AU  - Casadio, Rita
AU  - Boecker, Florian
AU  - Schoof, Heiko
AU  - Kahanda, Indika
AU  - Thurlby, Natalie
AU  - McHardy, Alice C
AU  - Renaux, Alexandre
AU  - Saidi, Rabie
AU  - Gough, Julian
AU  - Freitas, Alex A
AU  - Antczak, Magdalena
AU  - Fabris, Fabio
AU  - Wass, Mark N
AU  - Hou, Jie
AU  - Cheng, Jianlin
AU  - Wang, Zheng
AU  - Romero, Alfonso E
AU  - Paccanaro, Alberto
AU  - Yang, Haixuan
AU  - Goldberg, Tatyana
AU  - Zhao, Chenguang
AU  - Holm, Liisa
AU  - Törönen, Petri
AU  - Medlar, Alan J
AU  - Zosa, Elaine
AU  - Borukhov, Itamar
AU  - Novikov, Ilya
AU  - Wilkins, Angela
AU  - Lichtarge, Olivier
AU  - Chi, Po-Han
AU  - Tseng, Wei-Cheng
AU  - Linial, Michal
AU  - Rose, Peter W
AU  - Dessimoz, Christophe
AU  - Vidulin, Vedrana
AU  - Dzeroski, Saso
AU  - Sillitoe, Ian
AU  - Das, Sayoni
AU  - Lees, Jonathan Gill
AU  - Jones, David T
AU  - Wan, Cen
AU  - Cozzetto, Domenico
AU  - Fa, Rui
AU  - Torres, Mateo
AU  - Warwick Vesztrocy, Alex
AU  - Rodriguez, Jose Manuel
AU  - Tress, Michael L
AU  - Frasca, Marco
AU  - Notaro, Marco
AU  - Grossi, Giuliano
AU  - Petrini, Alessandro
AU  - Re, Matteo
AU  - Valentini, Giorgio
AU  - Mesiti, Marco
AU  - Roche, Daniel B
AU  - Reeb, Jonas
AU  - Ritchie, David W
AU  - Aridhi, Sabeur
AU  - Alborzi, Seyed Ziaeddin
AU  - Devignes, Marie-Dominique
AU  - Koo, Da Chen Emily
AU  - Bonneau, Richard
AU  - Gligorijević, Vladimir
AU  - Barot, Meet
AU  - Fang, Hai
AU  - Toppo, Stefano
AU  - Lavezzo, Enrico
AU  - Falda, Marco
AU  - Berselli, Michele
AU  - Tosatto, Silvio C.E.
AU  - Carraro, Marco
AU  - Piovesan, Damiano
AU  - Ur Rehman, Hafeez
AU  - Mao, Qizhong
AU  - Zhang, Shanshan
AU  - Vucetic, Slobodan
AU  - Black, Gage S
AU  - Jo, Dane
AU  - Suh, Erica
AU  - Dayton, Jonathan B
AU  - Larsen, Dallas J
AU  - Omdahl, Ashton R
AU  - McGuffin, Liam J
AU  - Brackenridge, Danielle A
AU  - Babbitt, Patricia C
AU  - Yunes, Jeffrey M
AU  - Fontana, Paolo
AU  - Zhang, Feng
AU  - Zhu, Shanfeng
AU  - You, Ronghui
AU  - Zhang, Zihan
AU  - Dai, Suyang
AU  - Yao, Shuwei
AU  - Tian, Weidong
AU  - Cao, Renzhi
AU  - Chandler, Caleb
AU  - Amezola, Miguel
AU  - Johnson, Devon
AU  - Chang, Jia-Ming
AU  - Liao, Wen-Hung
AU  - Liu, Yi-Wei
AU  - Pascarelli, Stefano
AU  - Frank, Yotam
AU  - Hoehndorf, Robert
AU  - Kulmanov, Maxat
AU  - Boudellioua, Imane
AU  - Politano, Gianfranco
AU  - Di Carlo, Stefano
AU  - Benso, Alfredo
AU  - Hakala, Kai
AU  - Ginter, Filip
AU  - Mehryary, Farrokh
AU  - Kaewphan, Suwisa
AU  - Björne, Jari
AU  - Moen, Hans
AU  - Tolvanen, Martti E.E.
AU  - Salakoski, Tapio
AU  - Kihara, Daisuke
AU  - Jain, Aashish
AU  - Šmuc, Tomislav
AU  - Altenhoff, Adrian
AU  - Ben-Hur, Asa
AU  - Rost, Burkhard
AU  - Brenner, Steven E
AU  - Orengo, Christine A
AU  - Jeffery, Constance J
AU  - Bosco, Giovanni
AU  - Hogan, Deborah A
AU  - Martin, Maria J
AU  - O’Donovan, Claire
AU  - Mooney, Sean D
AU  - Greene, Casey S
AU  - Radivojac, Predrag
AU  - Friedberg, Iddo
PY  - 2019
UR  - http://vinar.vin.bg.ac.rs/handle/123456789/8655
AB  - Background: The Critical Assessment of Functional Annotation (CAFA) is an ongoing, global, community-driven effort to evaluate and improve the computational annotation of protein function. Results: Here, we report on the results of the third CAFA challenge, CAFA3, that featured an expanded analysis over the previous CAFA rounds, both in terms of volume of data analyzed and the types of analysis performed. In a novel and major new development, computational predictions and assessment goals drove some of the experimental assays, resulting in new functional annotations for more than 1000 genes. Specifically, we performed experimental whole-genome mutation screening in Candida albicans and Pseudomonas aureginosa genomes, which provided us with genome-wide experimental data for genes associated with biofilm formation and motility. We further performed targeted assays on selected genes in Drosophila melanogaster, which we suspected of being involved in long-Term memory. Conclusion: We conclude that while predictions of the molecular function and biological process annotations have slightly improved over time, those of the cellular component have not. Term-centric prediction of experimental annotations remains equally challenging; although the performance of the top methods is significantly better than the expectations set by baseline methods in C. albicans and D. melanogaster, it leaves considerable room and need for improvement. Finally, we report that the CAFA community now involves a broad range of participants with expertise in bioinformatics, biological experimentation, biocuration, and bio-ontologies, working together to improve functional annotation, computational function prediction, and our ability to manage big data in the era of large experimental screens. © 2019 The Author(s).
T2  - Genome Biology
T1  - The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens
VL  - 20
IS  - 1
SP  - 244
DO  - 10.1186/s13059-019-1835-8
ER  - 
@article{
author = "Zhou, Naihui and Jiang, Yuxiang and Bergquist, Timothy R and Lee, Alexandra J and Kacsoh, Balint Z and Crocker, Alex W and Lewis, Kimberley A and Georghiou, George and Nguyen, Huy N and Hamid, Md Nafiz and Davis, Larry and Dogan, Tunca and Atalay, Volkan and Rifaioglu, Ahmet S and Dalkıran, Alperen and Cetin Atalay, Rengul and Zhang, Chengxin and Hurto, Rebecca L and Freddolino, Peter L and Zhang, Yang and Bhat, Prajwal and Supek, Fran and Fernández, José M and Gemović, Branislava S. and Perović, Vladimir R. and Davidović, Radoslav S. and Šumonja, Neven and Veljković, Nevena V. and Asgari, Ehsaneddin and Mofrad, Mohammad R.K. and Profiti, Giuseppe and Savojardo, Castrense and Martelli, Pier Luigi and Casadio, Rita and Boecker, Florian and Schoof, Heiko and Kahanda, Indika and Thurlby, Natalie and McHardy, Alice C and Renaux, Alexandre and Saidi, Rabie and Gough, Julian and Freitas, Alex A and Antczak, Magdalena and Fabris, Fabio and Wass, Mark N and Hou, Jie and Cheng, Jianlin and Wang, Zheng and Romero, Alfonso E and Paccanaro, Alberto and Yang, Haixuan and Goldberg, Tatyana and Zhao, Chenguang and Holm, Liisa and Törönen, Petri and Medlar, Alan J and Zosa, Elaine and Borukhov, Itamar and Novikov, Ilya and Wilkins, Angela and Lichtarge, Olivier and Chi, Po-Han and Tseng, Wei-Cheng and Linial, Michal and Rose, Peter W and Dessimoz, Christophe and Vidulin, Vedrana and Dzeroski, Saso and Sillitoe, Ian and Das, Sayoni and Lees, Jonathan Gill and Jones, David T and Wan, Cen and Cozzetto, Domenico and Fa, Rui and Torres, Mateo and Warwick Vesztrocy, Alex and Rodriguez, Jose Manuel and Tress, Michael L and Frasca, Marco and Notaro, Marco and Grossi, Giuliano and Petrini, Alessandro and Re, Matteo and Valentini, Giorgio and Mesiti, Marco and Roche, Daniel B and Reeb, Jonas and Ritchie, David W and Aridhi, Sabeur and Alborzi, Seyed Ziaeddin and Devignes, Marie-Dominique and Koo, Da Chen Emily and Bonneau, Richard and Gligorijević, Vladimir and Barot, Meet and Fang, Hai and Toppo, Stefano and Lavezzo, Enrico and Falda, Marco and Berselli, Michele and Tosatto, Silvio C.E. and Carraro, Marco and Piovesan, Damiano and Ur Rehman, Hafeez and Mao, Qizhong and Zhang, Shanshan and Vucetic, Slobodan and Black, Gage S and Jo, Dane and Suh, Erica and Dayton, Jonathan B and Larsen, Dallas J and Omdahl, Ashton R and McGuffin, Liam J and Brackenridge, Danielle A and Babbitt, Patricia C and Yunes, Jeffrey M and Fontana, Paolo and Zhang, Feng and Zhu, Shanfeng and You, Ronghui and Zhang, Zihan and Dai, Suyang and Yao, Shuwei and Tian, Weidong and Cao, Renzhi and Chandler, Caleb and Amezola, Miguel and Johnson, Devon and Chang, Jia-Ming and Liao, Wen-Hung and Liu, Yi-Wei and Pascarelli, Stefano and Frank, Yotam and Hoehndorf, Robert and Kulmanov, Maxat and Boudellioua, Imane and Politano, Gianfranco and Di Carlo, Stefano and Benso, Alfredo and Hakala, Kai and Ginter, Filip and Mehryary, Farrokh and Kaewphan, Suwisa and Björne, Jari and Moen, Hans and Tolvanen, Martti E.E. and Salakoski, Tapio and Kihara, Daisuke and Jain, Aashish and Šmuc, Tomislav and Altenhoff, Adrian and Ben-Hur, Asa and Rost, Burkhard and Brenner, Steven E and Orengo, Christine A and Jeffery, Constance J and Bosco, Giovanni and Hogan, Deborah A and Martin, Maria J and O’Donovan, Claire and Mooney, Sean D and Greene, Casey S and Radivojac, Predrag and Friedberg, Iddo",
year = "2019",
url = "http://vinar.vin.bg.ac.rs/handle/123456789/8655",
abstract = "Background: The Critical Assessment of Functional Annotation (CAFA) is an ongoing, global, community-driven effort to evaluate and improve the computational annotation of protein function. Results: Here, we report on the results of the third CAFA challenge, CAFA3, that featured an expanded analysis over the previous CAFA rounds, both in terms of volume of data analyzed and the types of analysis performed. In a novel and major new development, computational predictions and assessment goals drove some of the experimental assays, resulting in new functional annotations for more than 1000 genes. Specifically, we performed experimental whole-genome mutation screening in Candida albicans and Pseudomonas aureginosa genomes, which provided us with genome-wide experimental data for genes associated with biofilm formation and motility. We further performed targeted assays on selected genes in Drosophila melanogaster, which we suspected of being involved in long-Term memory. Conclusion: We conclude that while predictions of the molecular function and biological process annotations have slightly improved over time, those of the cellular component have not. Term-centric prediction of experimental annotations remains equally challenging; although the performance of the top methods is significantly better than the expectations set by baseline methods in C. albicans and D. melanogaster, it leaves considerable room and need for improvement. Finally, we report that the CAFA community now involves a broad range of participants with expertise in bioinformatics, biological experimentation, biocuration, and bio-ontologies, working together to improve functional annotation, computational function prediction, and our ability to manage big data in the era of large experimental screens. © 2019 The Author(s).",
journal = "Genome Biology",
title = "The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens",
volume = "20",
number = "1",
pages = "244",
doi = "10.1186/s13059-019-1835-8"
}
Zhou, N., Jiang, Y., Bergquist, T. R., Lee, A. J., Kacsoh, B. Z., Crocker, A. W., Lewis, K. A., Georghiou, G., Nguyen, H. N., Hamid, M. N., Davis, L., Dogan, T., Atalay, V., Rifaioglu, A. S., Dalkıran, A., Cetin Atalay, R., Zhang, C., Hurto, R. L., Freddolino, P. L., Zhang, Y., Bhat, P., Supek, F., Fernández, J. M., Gemović, B. S., Perović, V. R., Davidović, R. S., Šumonja, N., Veljković, N. V., Asgari, E., Mofrad, M. R.K., Profiti, G., Savojardo, C., Martelli, P. L., Casadio, R., Boecker, F., Schoof, H., Kahanda, I., Thurlby, N., McHardy, A. C., Renaux, A., Saidi, R., Gough, J., Freitas, A. A., Antczak, M., Fabris, F., Wass, M. N., Hou, J., Cheng, J., Wang, Z., Romero, A. E., Paccanaro, A., Yang, H., Goldberg, T., Zhao, C., Holm, L., Törönen, P., Medlar, A. J., Zosa, E., Borukhov, I., Novikov, I., Wilkins, A., Lichtarge, O., Chi, P., Tseng, W., Linial, M., Rose, P. W., Dessimoz, C., Vidulin, V., Dzeroski, S., Sillitoe, I., Das, S., Lees, J. G., Jones, D. T., Wan, C., Cozzetto, D., Fa, R., Torres, M., Warwick Vesztrocy, A., Rodriguez, J. M., Tress, M. L., Frasca, M., Notaro, M., Grossi, G., Petrini, A., Re, M., Valentini, G., Mesiti, M., Roche, D. B., Reeb, J., Ritchie, D. W., Aridhi, S., Alborzi, S. Z., Devignes, M., Koo, D. C. E., Bonneau, R., Gligorijević, V., Barot, M., Fang, H., Toppo, S., Lavezzo, E., Falda, M., Berselli, M., Tosatto, S. C.E., Carraro, M., Piovesan, D., Ur Rehman, H., Mao, Q., Zhang, S., Vucetic, S., Black, G. S., Jo, D., Suh, E., Dayton, J. B., Larsen, D. J., Omdahl, A. R., McGuffin, L. J., Brackenridge, D. A., Babbitt, P. C., Yunes, J. M., Fontana, P., Zhang, F., Zhu, S., You, R., Zhang, Z., Dai, S., Yao, S., Tian, W., Cao, R., Chandler, C., Amezola, M., Johnson, D., Chang, J., Liao, W., Liu, Y., Pascarelli, S., Frank, Y., Hoehndorf, R., Kulmanov, M., Boudellioua, I., Politano, G., Di Carlo, S., Benso, A., Hakala, K., Ginter, F., Mehryary, F., Kaewphan, S., Björne, J., Moen, H., Tolvanen, M. E.E., Salakoski, T., Kihara, D., Jain, A., Šmuc, T., Altenhoff, A., Ben-Hur, A., Rost, B., Brenner, S. E., Orengo, C. A., Jeffery, C. J., Bosco, G., Hogan, D. A., Martin, M. J., O’Donovan, C., Mooney, S. D., Greene, C. S., Radivojac, P.,& Friedberg, I. (2019). The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens.
Genome Biology, 20(1), 244.
https://doi.org/10.1186/s13059-019-1835-8
Zhou N, Jiang Y, Bergquist TR, Lee AJ, Kacsoh BZ, Crocker AW, Lewis KA, Georghiou G, Nguyen HN, Hamid MN, Davis L, Dogan T, Atalay V, Rifaioglu AS, Dalkıran A, Cetin Atalay R, Zhang C, Hurto RL, Freddolino PL, Zhang Y, Bhat P, Supek F, Fernández JM, Gemović BS, Perović VR, Davidović RS, Šumonja N, Veljković NV, Asgari E, Mofrad MR, Profiti G, Savojardo C, Martelli PL, Casadio R, Boecker F, Schoof H, Kahanda I, Thurlby N, McHardy AC, Renaux A, Saidi R, Gough J, Freitas AA, Antczak M, Fabris F, Wass MN, Hou J, Cheng J, Wang Z, Romero AE, Paccanaro A, Yang H, Goldberg T, Zhao C, Holm L, Törönen P, Medlar AJ, Zosa E, Borukhov I, Novikov I, Wilkins A, Lichtarge O, Chi P, Tseng W, Linial M, Rose PW, Dessimoz C, Vidulin V, Dzeroski S, Sillitoe I, Das S, Lees JG, Jones DT, Wan C, Cozzetto D, Fa R, Torres M, Warwick Vesztrocy A, Rodriguez JM, Tress ML, Frasca M, Notaro M, Grossi G, Petrini A, Re M, Valentini G, Mesiti M, Roche DB, Reeb J, Ritchie DW, Aridhi S, Alborzi SZ, Devignes M, Koo DCE, Bonneau R, Gligorijević V, Barot M, Fang H, Toppo S, Lavezzo E, Falda M, Berselli M, Tosatto SC, Carraro M, Piovesan D, Ur Rehman H, Mao Q, Zhang S, Vucetic S, Black GS, Jo D, Suh E, Dayton JB, Larsen DJ, Omdahl AR, McGuffin LJ, Brackenridge DA, Babbitt PC, Yunes JM, Fontana P, Zhang F, Zhu S, You R, Zhang Z, Dai S, Yao S, Tian W, Cao R, Chandler C, Amezola M, Johnson D, Chang J, Liao W, Liu Y, Pascarelli S, Frank Y, Hoehndorf R, Kulmanov M, Boudellioua I, Politano G, Di Carlo S, Benso A, Hakala K, Ginter F, Mehryary F, Kaewphan S, Björne J, Moen H, Tolvanen ME, Salakoski T, Kihara D, Jain A, Šmuc T, Altenhoff A, Ben-Hur A, Rost B, Brenner SE, Orengo CA, Jeffery CJ, Bosco G, Hogan DA, Martin MJ, O’Donovan C, Mooney SD, Greene CS, Radivojac P, Friedberg I. The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens. Genome Biology. 2019;20(1):244
Zhou Naihui, Jiang Yuxiang, Bergquist Timothy R, Lee Alexandra J, Kacsoh Balint Z, Crocker Alex W, Lewis Kimberley A, Georghiou George, Nguyen Huy N, Hamid Md Nafiz, Davis Larry, Dogan Tunca, Atalay Volkan, Rifaioglu Ahmet S, Dalkıran Alperen, Cetin Atalay Rengul, Zhang Chengxin, Hurto Rebecca L, Freddolino Peter L, Zhang Yang, Bhat Prajwal, Supek Fran, Fernández José M, Gemović Branislava S., Perović Vladimir R., Davidović Radoslav S., Šumonja Neven, Veljković Nevena V., Asgari Ehsaneddin, Mofrad Mohammad R.K., Profiti Giuseppe, Savojardo Castrense, Martelli Pier Luigi, Casadio Rita, Boecker Florian, Schoof Heiko, Kahanda Indika, Thurlby Natalie, McHardy Alice C, Renaux Alexandre, Saidi Rabie, Gough Julian, Freitas Alex A, Antczak Magdalena, Fabris Fabio, Wass Mark N, Hou Jie, Cheng Jianlin, Wang Zheng, Romero Alfonso E, Paccanaro Alberto, Yang Haixuan, Goldberg Tatyana, Zhao Chenguang, Holm Liisa, Törönen Petri, Medlar Alan J, Zosa Elaine, Borukhov Itamar, Novikov Ilya, Wilkins Angela, Lichtarge Olivier, Chi Po-Han, Tseng Wei-Cheng, Linial Michal, Rose Peter W, Dessimoz Christophe, Vidulin Vedrana, Dzeroski Saso, Sillitoe Ian, Das Sayoni, Lees Jonathan Gill, Jones David T, Wan Cen, Cozzetto Domenico, Fa Rui, Torres Mateo, Warwick Vesztrocy Alex, Rodriguez Jose Manuel, Tress Michael L, Frasca Marco, Notaro Marco, Grossi Giuliano, Petrini Alessandro, Re Matteo, Valentini Giorgio, Mesiti Marco, Roche Daniel B, Reeb Jonas, Ritchie David W, Aridhi Sabeur, Alborzi Seyed Ziaeddin, Devignes Marie-Dominique, Koo Da Chen Emily, Bonneau Richard, Gligorijević Vladimir, Barot Meet, Fang Hai, Toppo Stefano, Lavezzo Enrico, Falda Marco, Berselli Michele, Tosatto Silvio C.E., Carraro Marco, Piovesan Damiano, Ur Rehman Hafeez, Mao Qizhong, Zhang Shanshan, Vucetic Slobodan, Black Gage S, Jo Dane, Suh Erica, Dayton Jonathan B, Larsen Dallas J, Omdahl Ashton R, McGuffin Liam J, Brackenridge Danielle A, Babbitt Patricia C, Yunes Jeffrey M, Fontana Paolo, Zhang Feng, Zhu Shanfeng, You Ronghui, Zhang Zihan, Dai Suyang, Yao Shuwei, Tian Weidong, Cao Renzhi, Chandler Caleb, Amezola Miguel, Johnson Devon, Chang Jia-Ming, Liao Wen-Hung, Liu Yi-Wei, Pascarelli Stefano, Frank Yotam, Hoehndorf Robert, Kulmanov Maxat, Boudellioua Imane, Politano Gianfranco, Di Carlo Stefano, Benso Alfredo, Hakala Kai, Ginter Filip, Mehryary Farrokh, Kaewphan Suwisa, Björne Jari, Moen Hans, Tolvanen Martti E.E., Salakoski Tapio, Kihara Daisuke, Jain Aashish, Šmuc Tomislav, Altenhoff Adrian, Ben-Hur Asa, Rost Burkhard, Brenner Steven E, Orengo Christine A, Jeffery Constance J, Bosco Giovanni, Hogan Deborah A, Martin Maria J, O’Donovan Claire, Mooney Sean D, Greene Casey S, Radivojac Predrag, Friedberg Iddo, "The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens" Genome Biology, 20, no. 1 (2019):244,
https://doi.org/10.1186/s13059-019-1835-8 .
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Virtual Screen for Repurposing of Drugs for Candidate Influenza a M2 Ion-Channel Inhibitors

Radošević, Draginja; Senćanski, Milan V.; Perović, Vladimir R.; Veljković, Nevena V.; Prljić, Jelena; Veljković, Veljko; Mantlo, Emily; Bukreyeva, Natalya; Paessler, Slobodan; Glišić, Sanja

(2019)

TY  - JOUR
AU  - Radošević, Draginja
AU  - Senćanski, Milan V.
AU  - Perović, Vladimir R.
AU  - Veljković, Nevena V.
AU  - Prljić, Jelena
AU  - Veljković, Veljko
AU  - Mantlo, Emily
AU  - Bukreyeva, Natalya
AU  - Paessler, Slobodan
AU  - Glišić, Sanja
PY  - 2019
UR  - https://www.frontiersin.org/article/10.3389/fcimb.2019.00067/full
UR  - http://vinar.vin.bg.ac.rs/handle/123456789/8163
AB  - Influenza A virus (IAV) matrix protein 2 (M2), an ion channel, is crucial for virus infection, and therefore, an important anti-influenza drug target. Adamantanes, also known as M2 channel blockers, are one of the two classes of Food and Drug Administration-approved anti-influenza drugs, although their use was discontinued due to prevalent drug resistance. Fast emergence of resistance to current anti-influenza drugs have raised an urgent need for developing new anti-influenza drugs against resistant forms of circulating viruses. Here we propose a simple theoretical criterion for fast virtual screening of molecular libraries for candidate anti-influenza ion channel inhibitors both for wild type and adamantane-resistant influenza A viruses. After in silico screening of drug space using the EIIP/AQVN filter and further filtering of drugs by ligand based virtual screening and molecular docking we propose the best candidate drugs as potential dual inhibitors of wild type and adamantane-resistant influenza A viruses. Finally, guanethidine, the best ranked drug selected from ligand-based virtual screening, was experimentally tested. The experimental results show measurable anti-influenza activity of guanethidine in cell culture. © 2019 Radosevic, Sencanski, Perovic, Veljkovic, Prljic, Veljkovic, Mantlo, Bukreyeva, Paessler and Glisic.
T2  - Frontiers in Cellular and Infection Microbiology
T1  - Virtual Screen for Repurposing of Drugs for Candidate Influenza a M2 Ion-Channel Inhibitors
VL  - 9
IS  - MAR
DO  - 10.3389/fcimb.2019.00067
ER  - 
@article{
author = "Radošević, Draginja and Senćanski, Milan V. and Perović, Vladimir R. and Veljković, Nevena V. and Prljić, Jelena and Veljković, Veljko and Mantlo, Emily and Bukreyeva, Natalya and Paessler, Slobodan and Glišić, Sanja",
year = "2019",
url = "https://www.frontiersin.org/article/10.3389/fcimb.2019.00067/full, http://vinar.vin.bg.ac.rs/handle/123456789/8163",
abstract = "Influenza A virus (IAV) matrix protein 2 (M2), an ion channel, is crucial for virus infection, and therefore, an important anti-influenza drug target. Adamantanes, also known as M2 channel blockers, are one of the two classes of Food and Drug Administration-approved anti-influenza drugs, although their use was discontinued due to prevalent drug resistance. Fast emergence of resistance to current anti-influenza drugs have raised an urgent need for developing new anti-influenza drugs against resistant forms of circulating viruses. Here we propose a simple theoretical criterion for fast virtual screening of molecular libraries for candidate anti-influenza ion channel inhibitors both for wild type and adamantane-resistant influenza A viruses. After in silico screening of drug space using the EIIP/AQVN filter and further filtering of drugs by ligand based virtual screening and molecular docking we propose the best candidate drugs as potential dual inhibitors of wild type and adamantane-resistant influenza A viruses. Finally, guanethidine, the best ranked drug selected from ligand-based virtual screening, was experimentally tested. The experimental results show measurable anti-influenza activity of guanethidine in cell culture. © 2019 Radosevic, Sencanski, Perovic, Veljkovic, Prljic, Veljkovic, Mantlo, Bukreyeva, Paessler and Glisic.",
journal = "Frontiers in Cellular and Infection Microbiology",
title = "Virtual Screen for Repurposing of Drugs for Candidate Influenza a M2 Ion-Channel Inhibitors",
volume = "9",
number = "MAR",
doi = "10.3389/fcimb.2019.00067"
}
Radošević, D., Senćanski, M. V., Perović, V. R., Veljković, N. V., Prljić, J., Veljković, V., Mantlo, E., Bukreyeva, N., Paessler, S.,& Glišić, S. (2019). Virtual Screen for Repurposing of Drugs for Candidate Influenza a M2 Ion-Channel Inhibitors.
Frontiers in Cellular and Infection Microbiology, 9(MAR).
https://doi.org/10.3389/fcimb.2019.00067
Radošević D, Senćanski MV, Perović VR, Veljković NV, Prljić J, Veljković V, Mantlo E, Bukreyeva N, Paessler S, Glišić S. Virtual Screen for Repurposing of Drugs for Candidate Influenza a M2 Ion-Channel Inhibitors. Frontiers in Cellular and Infection Microbiology. 2019;9(MAR)
Radošević Draginja, Senćanski Milan V., Perović Vladimir R., Veljković Nevena V., Prljić Jelena, Veljković Veljko, Mantlo Emily, Bukreyeva Natalya, Paessler Slobodan, Glišić Sanja, "Virtual Screen for Repurposing of Drugs for Candidate Influenza a M2 Ion-Channel Inhibitors" Frontiers in Cellular and Infection Microbiology, 9, no. MAR (2019),
https://doi.org/10.3389/fcimb.2019.00067 .
1
5
4
4

Automated feature engineering improves prediction of protein–protein interactions

Šumonja, Neven; Gemović, Branislava S.; Veljković, Nevena V.; Perović, Vladimir R.

(2019)

TY  - JOUR
AU  - Šumonja, Neven
AU  - Gemović, Branislava S.
AU  - Veljković, Nevena V.
AU  - Perović, Vladimir R.
PY  - 2019
UR  - http://vinar.vin.bg.ac.rs/handle/123456789/8395
AB  - Over the last decade, various machine learning (ML) and statistical approaches for protein–protein interaction (PPI) predictions have been developed to help annotating functional interactions among proteins, essential for our system-level understanding of life. Efficient ML approaches require informative and non-redundant features. In this paper, we introduce novel types of expert-crafted sequence, evolutionary and graph features and apply automatic feature engineering to further expand feature space to improve predictive modeling. The two-step automatic feature-engineering process encompasses the hybrid method for feature generation and unsupervised feature selection, followed by supervised feature selection through a genetic algorithm (GA). The optimization of both steps allows the feature-engineering procedure to operate on a large transformed feature space with no considerable computational cost and to efficiently provide newly engineered features. Based on GA and correlation filtering, we developed a stacking algorithm GA-STACK for automatic ensembling of different ML algorithms to improve prediction performance. We introduced a unified method, HP-GAS, for the prediction of human PPIs, which incorporates GA-STACK and rests on both expert-crafted and 40% of newly engineered features. The extensive cross validation and comparison with the state-of-the-art methods showed that HP-GAS represents currently the most efficient method for proteome-wide forecasting of protein interactions, with prediction efficacy of 0.93 AUC and 0.85 accuracy. We implemented the HP-GAS method as a free standalone application which is a time-efficient and easy-to-use tool. HP-GAS software with supplementary data can be downloaded from: http://www.vinca.rs/180/tools/HP-GAS.php. © 2019, Springer-Verlag GmbH Austria, part of Springer Nature.
T2  - Amino Acids
T1  - Automated feature engineering improves prediction of protein–protein interactions
VL  - 51
IS  - 8
SP  - 1187
EP  - 1200
DO  - 10.1007/s00726-019-02756-9
ER  - 
@article{
author = "Šumonja, Neven and Gemović, Branislava S. and Veljković, Nevena V. and Perović, Vladimir R.",
year = "2019",
url = "http://vinar.vin.bg.ac.rs/handle/123456789/8395",
abstract = "Over the last decade, various machine learning (ML) and statistical approaches for protein–protein interaction (PPI) predictions have been developed to help annotating functional interactions among proteins, essential for our system-level understanding of life. Efficient ML approaches require informative and non-redundant features. In this paper, we introduce novel types of expert-crafted sequence, evolutionary and graph features and apply automatic feature engineering to further expand feature space to improve predictive modeling. The two-step automatic feature-engineering process encompasses the hybrid method for feature generation and unsupervised feature selection, followed by supervised feature selection through a genetic algorithm (GA). The optimization of both steps allows the feature-engineering procedure to operate on a large transformed feature space with no considerable computational cost and to efficiently provide newly engineered features. Based on GA and correlation filtering, we developed a stacking algorithm GA-STACK for automatic ensembling of different ML algorithms to improve prediction performance. We introduced a unified method, HP-GAS, for the prediction of human PPIs, which incorporates GA-STACK and rests on both expert-crafted and 40% of newly engineered features. The extensive cross validation and comparison with the state-of-the-art methods showed that HP-GAS represents currently the most efficient method for proteome-wide forecasting of protein interactions, with prediction efficacy of 0.93 AUC and 0.85 accuracy. We implemented the HP-GAS method as a free standalone application which is a time-efficient and easy-to-use tool. HP-GAS software with supplementary data can be downloaded from: http://www.vinca.rs/180/tools/HP-GAS.php. © 2019, Springer-Verlag GmbH Austria, part of Springer Nature.",
journal = "Amino Acids",
title = "Automated feature engineering improves prediction of protein–protein interactions",
volume = "51",
number = "8",
pages = "1187-1200",
doi = "10.1007/s00726-019-02756-9"
}
Šumonja, N., Gemović, B. S., Veljković, N. V.,& Perović, V. R. (2019). Automated feature engineering improves prediction of protein–protein interactions.
Amino Acids, 51(8), 1187-1200.
https://doi.org/10.1007/s00726-019-02756-9
Šumonja N, Gemović BS, Veljković NV, Perović VR. Automated feature engineering improves prediction of protein–protein interactions. Amino Acids. 2019;51(8):1187-1200
Šumonja Neven, Gemović Branislava S., Veljković Nevena V., Perović Vladimir R., "Automated feature engineering improves prediction of protein–protein interactions" Amino Acids, 51, no. 8 (2019):1187-1200,
https://doi.org/10.1007/s00726-019-02756-9 .
1
8
2
6

IDPpi: Protein-Protein Interaction Analyses of Human Intrinsically Disordered Proteins

Perović, Vladimir R.; Šumonja, Neven; Marsh, Lindsey A.; Radovanović, Sandro; Vukićević, Milan; Roberts, Stefan G. E.; Veljković, Nevena V.

(2018)

TY  - JOUR
AU  - Perović, Vladimir R.
AU  - Šumonja, Neven
AU  - Marsh, Lindsey A.
AU  - Radovanović, Sandro
AU  - Vukićević, Milan
AU  - Roberts, Stefan G. E.
AU  - Veljković, Nevena V.
PY  - 2018
UR  - http://www.nature.com/articles/s41598-018-28815-x
UR  - http://vinar.vin.bg.ac.rs/handle/123456789/7811
AB  - Intrinsically disordered proteins (IDPs) are characterized by the lack of a fixed tertiary structure and are involved in the regulation of key biological processes via binding to multiple protein partners. IDPs are malleable, adapting to structurally different partners, and this flexibility stems from features encoded in the primary structure. The assumption that universal sequence information will facilitate coverage of the sparse zones of the human interactome motivated us to explore the possibility of predicting protein-protein interactions (PPIs) that involve IDPs based on sequence characteristics. We developed a method that relies on features of the interacting and non-interacting protein pairs and utilizes machine learning to classify and predict IDP PPIs. Consideration of both sequence determinants specific for conformational organizations and the multiplicity of IDP interactions in the training phase ensured a reliable approach that is superior to current state-of-the-art methods. By applying a strict evaluation procedure, we confirm that our method predicts interactions of the IDP of interest even on the proteome-scale. This service is provided as a web tool to expedite the discovery of new interactions and IDP functions with enhanced efficiency. © 2018 The Author(s).
T2  - Scientific Reports
T1  - IDPpi: Protein-Protein Interaction Analyses of Human Intrinsically Disordered Proteins
VL  - 8
IS  - 1
SP  - 10563
DO  - 10.1038/s41598-018-28815-x
ER  - 
@article{
author = "Perović, Vladimir R. and Šumonja, Neven and Marsh, Lindsey A. and Radovanović, Sandro and Vukićević, Milan and Roberts, Stefan G. E. and Veljković, Nevena V.",
year = "2018",
url = "http://www.nature.com/articles/s41598-018-28815-x, http://vinar.vin.bg.ac.rs/handle/123456789/7811",
abstract = "Intrinsically disordered proteins (IDPs) are characterized by the lack of a fixed tertiary structure and are involved in the regulation of key biological processes via binding to multiple protein partners. IDPs are malleable, adapting to structurally different partners, and this flexibility stems from features encoded in the primary structure. The assumption that universal sequence information will facilitate coverage of the sparse zones of the human interactome motivated us to explore the possibility of predicting protein-protein interactions (PPIs) that involve IDPs based on sequence characteristics. We developed a method that relies on features of the interacting and non-interacting protein pairs and utilizes machine learning to classify and predict IDP PPIs. Consideration of both sequence determinants specific for conformational organizations and the multiplicity of IDP interactions in the training phase ensured a reliable approach that is superior to current state-of-the-art methods. By applying a strict evaluation procedure, we confirm that our method predicts interactions of the IDP of interest even on the proteome-scale. This service is provided as a web tool to expedite the discovery of new interactions and IDP functions with enhanced efficiency. © 2018 The Author(s).",
journal = "Scientific Reports",
title = "IDPpi: Protein-Protein Interaction Analyses of Human Intrinsically Disordered Proteins",
volume = "8",
number = "1",
pages = "10563",
doi = "10.1038/s41598-018-28815-x"
}
Perović, V. R., Šumonja, N., Marsh, L. A., Radovanović, S., Vukićević, M., Roberts, S. G. E.,& Veljković, N. V. (2018). IDPpi: Protein-Protein Interaction Analyses of Human Intrinsically Disordered Proteins.
Scientific Reports, 8(1), 10563.
https://doi.org/10.1038/s41598-018-28815-x
Perović VR, Šumonja N, Marsh LA, Radovanović S, Vukićević M, Roberts SGE, Veljković NV. IDPpi: Protein-Protein Interaction Analyses of Human Intrinsically Disordered Proteins. Scientific Reports. 2018;8(1):10563
Perović Vladimir R., Šumonja Neven, Marsh Lindsey A., Radovanović Sandro, Vukićević Milan, Roberts Stefan G. E., Veljković Nevena V., "IDPpi: Protein-Protein Interaction Analyses of Human Intrinsically Disordered Proteins" Scientific Reports, 8, no. 1 (2018):10563,
https://doi.org/10.1038/s41598-018-28815-x .
4
6
4
4

Ibuprofen as a template molecule for drug design against Ebola virus

Paessler, Slobodan; Huang, Cheng; Senćanski, Milan V.; Veljković, Nevena V.; Perović, Vladimir R.; Glišić, Sanja; Veljković, Veljko

(2018)

TY  - JOUR
AU  - Paessler, Slobodan
AU  - Huang, Cheng
AU  - Senćanski, Milan V.
AU  - Veljković, Nevena V.
AU  - Perović, Vladimir R.
AU  - Glišić, Sanja
AU  - Veljković, Veljko
PY  - 2018
UR  - http://vinar.vin.bg.ac.rs/handle/123456789/7695
AB  - The Ebola virus outbreak in West Africa 2015 and Congo 2017, point out an urgent need for development of drugs against this important pathogen. Previously, by repurposing virtual screening of 6438 drugs from DrugBank, ibuprofen was selected as a possible inhibitor of the Ebola virus infection. The results of an additional docking analysis as well as experimental results showing measurable anti-Ebola effect of ibuprofen in cell culture suggest ibuprofen as a promising molecular template for the development of drugs for treatment of the infection by Ebola virus.
T2  - Frontiers in Bioscience - Landmark
T1  - Ibuprofen as a template molecule for drug design against Ebola virus
VL  - 23
IS  - 5
SP  - 947
EP  - 953
ER  - 
@article{
author = "Paessler, Slobodan and Huang, Cheng and Senćanski, Milan V. and Veljković, Nevena V. and Perović, Vladimir R. and Glišić, Sanja and Veljković, Veljko",
year = "2018",
url = "http://vinar.vin.bg.ac.rs/handle/123456789/7695",
abstract = "The Ebola virus outbreak in West Africa 2015 and Congo 2017, point out an urgent need for development of drugs against this important pathogen. Previously, by repurposing virtual screening of 6438 drugs from DrugBank, ibuprofen was selected as a possible inhibitor of the Ebola virus infection. The results of an additional docking analysis as well as experimental results showing measurable anti-Ebola effect of ibuprofen in cell culture suggest ibuprofen as a promising molecular template for the development of drugs for treatment of the infection by Ebola virus.",
journal = "Frontiers in Bioscience - Landmark",
title = "Ibuprofen as a template molecule for drug design against Ebola virus",
volume = "23",
number = "5",
pages = "947-953"
}
Paessler, S., Huang, C., Senćanski, M. V., Veljković, N. V., Perović, V. R., Glišić, S.,& Veljković, V. (2018). Ibuprofen as a template molecule for drug design against Ebola virus.
Frontiers in Bioscience - Landmark, 23(5), 947-953.
Paessler S, Huang C, Senćanski MV, Veljković NV, Perović VR, Glišić S, Veljković V. Ibuprofen as a template molecule for drug design against Ebola virus. Frontiers in Bioscience - Landmark. 2018;23(5):947-953
Paessler Slobodan, Huang Cheng, Senćanski Milan V., Veljković Nevena V., Perović Vladimir R., Glišić Sanja, Veljković Veljko, "Ibuprofen as a template molecule for drug design against Ebola virus" Frontiers in Bioscience - Landmark, 23, no. 5 (2018):947-953
13

TRI_tool: a web-tool for prediction of protein-protein interactions in human transcriptional regulation

Perović, Vladimir R.; Šumonja, Neven; Gemović, Branislava S.; Toska, Eneda; Roberts, Stefan G. E.; Veljković, Nevena V.

(2017)

TY  - JOUR
AU  - Perović, Vladimir R.
AU  - Šumonja, Neven
AU  - Gemović, Branislava S.
AU  - Toska, Eneda
AU  - Roberts, Stefan G. E.
AU  - Veljković, Nevena V.
PY  - 2017
UR  - http://vinar.vin.bg.ac.rs/handle/123456789/1468
AB  - The TRI_tool, a sequence-based web tool for prediction of protein interactions in the human transcriptional regulation, is intended for biomedical investigators who work on understanding the regulation of gene expression. It has an improved predictive performance due to the training on updated, human specific, experimentally validated datasets. The TRI_tool is designed to test up to 100 potential interactions with no time delay and to report both probabilities and binarized predictions.
T2  - Bioinformatics
T1  - TRI_tool: a web-tool for prediction of protein-protein interactions in human transcriptional regulation
VL  - 33
IS  - 2
SP  - 289
EP  - 291
DO  - 10.1093/bioinformatics/btw590
ER  - 
@article{
author = "Perović, Vladimir R. and Šumonja, Neven and Gemović, Branislava S. and Toska, Eneda and Roberts, Stefan G. E. and Veljković, Nevena V.",
year = "2017",
url = "http://vinar.vin.bg.ac.rs/handle/123456789/1468",
abstract = "The TRI_tool, a sequence-based web tool for prediction of protein interactions in the human transcriptional regulation, is intended for biomedical investigators who work on understanding the regulation of gene expression. It has an improved predictive performance due to the training on updated, human specific, experimentally validated datasets. The TRI_tool is designed to test up to 100 potential interactions with no time delay and to report both probabilities and binarized predictions.",
journal = "Bioinformatics",
title = "TRI_tool: a web-tool for prediction of protein-protein interactions in human transcriptional regulation",
volume = "33",
number = "2",
pages = "289-291",
doi = "10.1093/bioinformatics/btw590"
}
Perović, V. R., Šumonja, N., Gemović, B. S., Toska, E., Roberts, S. G. E.,& Veljković, N. V. (2017). TRI_tool: a web-tool for prediction of protein-protein interactions in human transcriptional regulation.
Bioinformatics, 33(2), 289-291.
https://doi.org/10.1093/bioinformatics/btw590
Perović VR, Šumonja N, Gemović BS, Toska E, Roberts SGE, Veljković NV. TRI_tool: a web-tool for prediction of protein-protein interactions in human transcriptional regulation. Bioinformatics. 2017;33(2):289-291
Perović Vladimir R., Šumonja Neven, Gemović Branislava S., Toska Eneda, Roberts Stefan G. E., Veljković Nevena V., "TRI_tool: a web-tool for prediction of protein-protein interactions in human transcriptional regulation" Bioinformatics, 33, no. 2 (2017):289-291,
https://doi.org/10.1093/bioinformatics/btw590 .
1
7
5
6

Identification of Candidate Allosteric Modulators of the M1 Muscarinic Acetylcholine Receptor Which May Improve Vagus Nerve Stimulation in ChronicTinnitus

Bojić, Tijana; Perović, Vladimir R.; Senćanski, Milan V.; Glišić, Sanja

(2017)

TY  - JOUR
AU  - Bojić, Tijana
AU  - Perović, Vladimir R.
AU  - Senćanski, Milan V.
AU  - Glišić, Sanja
PY  - 2017
UR  - http://vinar.vin.bg.ac.rs/handle/123456789/1823
AB  - Chronic tinnitus is characterized by neuroplastic changes of the auditory cortex. A promising method for therapy of chronic tinnitus is vagus nerve stimulation (VNS) combined with auditory stimulation. The principle of VNS is reversal of pathological neuroplastic changes of the auditory cortex toward physiological neural activity and synchronicity. The VNS mechanism of action in chronic tinnitus patients is prevailingly through the muscarinic neuromodulation of the auditory cortex by the activation of nc. basalis Meynerti. The aim of this study is to propose potential pharmaceutics which may improve the neuromodulatory effects of VNS. The working hypothesis is that M1 receptors have a dominant role in the neural plasticity of the auditory cortex. We propose that allosteric agonists of the muscarinic receptor type 1 (M1) receptor could improve specificity and selectivity of the neuromodulatory effect of VNS on the auditory cortex of chronic tinnitus patients even in the circumstances of lower acetylcholine brain concentration. This intervention would also reinforce the re-learning process of tinnitus (sub) networks by acting on cholinergic memory and learning mechanisms. We performed in silico screening of drug space using the EIIP/AQVN filter and selected 50 drugs as candidates for allosteric modulators of muscarinic receptors. Further filtering of these compounds by means of 3D QSAR and docking revealed 3 approved drugs-bromazepam, estazolam and flumazenil as the most promising candidates for combined chronic tinnitus therapy. These drugs should be further evaluated by biological tests and clinical trials.
T2  - Frontiers in Neuroscience
T1  - Identification of Candidate Allosteric Modulators of the M1 Muscarinic Acetylcholine Receptor Which May Improve Vagus Nerve Stimulation in ChronicTinnitus
VL  - 11
SP  - 636
DO  - 10.3389/fnins.2017.00636
ER  - 
@article{
author = "Bojić, Tijana and Perović, Vladimir R. and Senćanski, Milan V. and Glišić, Sanja",
year = "2017",
url = "http://vinar.vin.bg.ac.rs/handle/123456789/1823",
abstract = "Chronic tinnitus is characterized by neuroplastic changes of the auditory cortex. A promising method for therapy of chronic tinnitus is vagus nerve stimulation (VNS) combined with auditory stimulation. The principle of VNS is reversal of pathological neuroplastic changes of the auditory cortex toward physiological neural activity and synchronicity. The VNS mechanism of action in chronic tinnitus patients is prevailingly through the muscarinic neuromodulation of the auditory cortex by the activation of nc. basalis Meynerti. The aim of this study is to propose potential pharmaceutics which may improve the neuromodulatory effects of VNS. The working hypothesis is that M1 receptors have a dominant role in the neural plasticity of the auditory cortex. We propose that allosteric agonists of the muscarinic receptor type 1 (M1) receptor could improve specificity and selectivity of the neuromodulatory effect of VNS on the auditory cortex of chronic tinnitus patients even in the circumstances of lower acetylcholine brain concentration. This intervention would also reinforce the re-learning process of tinnitus (sub) networks by acting on cholinergic memory and learning mechanisms. We performed in silico screening of drug space using the EIIP/AQVN filter and selected 50 drugs as candidates for allosteric modulators of muscarinic receptors. Further filtering of these compounds by means of 3D QSAR and docking revealed 3 approved drugs-bromazepam, estazolam and flumazenil as the most promising candidates for combined chronic tinnitus therapy. These drugs should be further evaluated by biological tests and clinical trials.",
journal = "Frontiers in Neuroscience",
title = "Identification of Candidate Allosteric Modulators of the M1 Muscarinic Acetylcholine Receptor Which May Improve Vagus Nerve Stimulation in ChronicTinnitus",
volume = "11",
pages = "636",
doi = "10.3389/fnins.2017.00636"
}
Bojić, T., Perović, V. R., Senćanski, M. V.,& Glišić, S. (2017). Identification of Candidate Allosteric Modulators of the M1 Muscarinic Acetylcholine Receptor Which May Improve Vagus Nerve Stimulation in ChronicTinnitus.
Frontiers in Neuroscience, 11, 636.
https://doi.org/10.3389/fnins.2017.00636
Bojić T, Perović VR, Senćanski MV, Glišić S. Identification of Candidate Allosteric Modulators of the M1 Muscarinic Acetylcholine Receptor Which May Improve Vagus Nerve Stimulation in ChronicTinnitus. Frontiers in Neuroscience. 2017;11:636
Bojić Tijana, Perović Vladimir R., Senćanski Milan V., Glišić Sanja, "Identification of Candidate Allosteric Modulators of the M1 Muscarinic Acetylcholine Receptor Which May Improve Vagus Nerve Stimulation in ChronicTinnitus" Frontiers in Neuroscience, 11 (2017):636,
https://doi.org/10.3389/fnins.2017.00636 .
2
3
3
3

Predicted Enhanced Human Propensity of Current Avian-Like H1N1 Swine Influenza Virus from China

Veljković, Veljko; Veljković, Nevena V.; Paessler, Slobodan; Goeijenbier, Marco; Perović, Vladimir R.; Glišić, Sanja; Muller, Claude P.

(2016)

TY  - JOUR
AU  - Veljković, Veljko
AU  - Veljković, Nevena V.
AU  - Paessler, Slobodan
AU  - Goeijenbier, Marco
AU  - Perović, Vladimir R.
AU  - Glišić, Sanja
AU  - Muller, Claude P.
PY  - 2016
UR  - http://vinar.vin.bg.ac.rs/handle/123456789/1300
AB  - Influenza A virus (IAV) subtypes against which little or no pre-existing immunity exists in humans represent a serious threat to global public health. Monitoring of IAV in animal hosts is essential for early and rapid detection of potential pandemic IAV strains to prevent their spread. Recently, the increased pandemic potential of the avian-like swine H1N1 IAV A/swine/Guangdong/104/2013 has been suggested. The virus is infectious in humans and the general population seems to lack neutralizing antibodies against this virus. Here we present an in silico analysis that shows a strong human propensity of this swine virus further confirming its pandemic potential. We suggest mutations which would further enhance its human propensity. We also propose conserved antigenic determinants which could serve as a component of a prepandemic vaccine. The bioinformatics tool, which can be used to further monitor the evolution of swine influenza viruses towards a pandemic virus, are described here and are made publically available (http://www.vin.bg.ac.rs/180/tools/iav_ mon.php;http://www.biomedprotection.com/iav_mon.php).
T2  - PLOS One
T1  - Predicted Enhanced Human Propensity of Current Avian-Like H1N1 Swine Influenza Virus from China
VL  - 11
IS  - 11
DO  - 10.1371/journal.pone.0165451
ER  - 
@article{
author = "Veljković, Veljko and Veljković, Nevena V. and Paessler, Slobodan and Goeijenbier, Marco and Perović, Vladimir R. and Glišić, Sanja and Muller, Claude P.",
year = "2016",
url = "http://vinar.vin.bg.ac.rs/handle/123456789/1300",
abstract = "Influenza A virus (IAV) subtypes against which little or no pre-existing immunity exists in humans represent a serious threat to global public health. Monitoring of IAV in animal hosts is essential for early and rapid detection of potential pandemic IAV strains to prevent their spread. Recently, the increased pandemic potential of the avian-like swine H1N1 IAV A/swine/Guangdong/104/2013 has been suggested. The virus is infectious in humans and the general population seems to lack neutralizing antibodies against this virus. Here we present an in silico analysis that shows a strong human propensity of this swine virus further confirming its pandemic potential. We suggest mutations which would further enhance its human propensity. We also propose conserved antigenic determinants which could serve as a component of a prepandemic vaccine. The bioinformatics tool, which can be used to further monitor the evolution of swine influenza viruses towards a pandemic virus, are described here and are made publically available (http://www.vin.bg.ac.rs/180/tools/iav_ mon.php;http://www.biomedprotection.com/iav_mon.php).",
journal = "PLOS One",
title = "Predicted Enhanced Human Propensity of Current Avian-Like H1N1 Swine Influenza Virus from China",
volume = "11",
number = "11",
doi = "10.1371/journal.pone.0165451"
}
Veljković, V., Veljković, N. V., Paessler, S., Goeijenbier, M., Perović, V. R., Glišić, S.,& Muller, C. P. (2016). Predicted Enhanced Human Propensity of Current Avian-Like H1N1 Swine Influenza Virus from China.
PLOS One, 11(11).
https://doi.org/10.1371/journal.pone.0165451
Veljković V, Veljković NV, Paessler S, Goeijenbier M, Perović VR, Glišić S, Muller CP. Predicted Enhanced Human Propensity of Current Avian-Like H1N1 Swine Influenza Virus from China. PLOS One. 2016;11(11)
Veljković Veljko, Veljković Nevena V., Paessler Slobodan, Goeijenbier Marco, Perović Vladimir R., Glišić Sanja, Muller Claude P., "Predicted Enhanced Human Propensity of Current Avian-Like H1N1 Swine Influenza Virus from China" PLOS One, 11, no. 11 (2016),
https://doi.org/10.1371/journal.pone.0165451 .
2
2
1

An expanded evaluation of protein function prediction methods shows an improvement in accuracy

Jiang, Yuxiang; Gemović, Branislava S.; Glišić, Sanja; Perović, Vladimir R.; Veljković, Veljko; Veljković, Nevena V.

(2016)

TY  - JOUR
AU  - Jiang, Yuxiang
AU  - Gemović, Branislava S.
AU  - Glišić, Sanja
AU  - Perović, Vladimir R.
AU  - Veljković, Veljko
AU  - Veljković, Nevena V.
PY  - 2016
UR  - http://vinar.vin.bg.ac.rs/handle/123456789/1244
AB  - Background: A major bottleneck in our understanding of the molecular underpinnings of life is the assignment of function to proteins. While molecular experiments provide the most reliable annotation of proteins, their relatively low throughput and restricted purview have led to an increasing role for computational function prediction. However, assessing methods for protein function prediction and tracking progress in the field remain challenging. Results: We conducted the second critical assessment of functional annotation (CAFA), a timed challenge to assess computational methods that automatically assign protein function. We evaluated 126 methods from 56 research groups for their ability to predict biological functions using Gene Ontology and gene-disease associations using Human Phenotype Ontology on a set of 3681 proteins from 18 species. CAFA2 featured expanded analysis compared with CAFA1, with regards to data set size, variety, and assessment metrics. To review progress in the field, the analysis compared the best methods from CAFA1 to those of CAFA2. Conclusions: The top-performing methods in CAFA2 outperformed those from CAFA1. This increased accuracy can be attributed to a combination of the growing number of experimental annotations and improved methods for function prediction. The assessment also revealed that the definition of top-performing algorithms is ontology specific, that different performance metrics can be used to probe the nature of accurate predictions, and the relative diversity of predictions in the biological process and human phenotype ontologies. While there was methodological improvement between CAFA1 and CAFA2, the interpretation of results and usefulness of individual methods remain context-dependent.
T2  - Genome Biology
T1  - An expanded evaluation of protein function prediction methods shows an improvement in accuracy
VL  - 17
DO  - 10.1186/s13059-016-1037-6
ER  - 
@article{
author = "Jiang, Yuxiang and Gemović, Branislava S. and Glišić, Sanja and Perović, Vladimir R. and Veljković, Veljko and Veljković, Nevena V.",
year = "2016",
url = "http://vinar.vin.bg.ac.rs/handle/123456789/1244",
abstract = "Background: A major bottleneck in our understanding of the molecular underpinnings of life is the assignment of function to proteins. While molecular experiments provide the most reliable annotation of proteins, their relatively low throughput and restricted purview have led to an increasing role for computational function prediction. However, assessing methods for protein function prediction and tracking progress in the field remain challenging. Results: We conducted the second critical assessment of functional annotation (CAFA), a timed challenge to assess computational methods that automatically assign protein function. We evaluated 126 methods from 56 research groups for their ability to predict biological functions using Gene Ontology and gene-disease associations using Human Phenotype Ontology on a set of 3681 proteins from 18 species. CAFA2 featured expanded analysis compared with CAFA1, with regards to data set size, variety, and assessment metrics. To review progress in the field, the analysis compared the best methods from CAFA1 to those of CAFA2. Conclusions: The top-performing methods in CAFA2 outperformed those from CAFA1. This increased accuracy can be attributed to a combination of the growing number of experimental annotations and improved methods for function prediction. The assessment also revealed that the definition of top-performing algorithms is ontology specific, that different performance metrics can be used to probe the nature of accurate predictions, and the relative diversity of predictions in the biological process and human phenotype ontologies. While there was methodological improvement between CAFA1 and CAFA2, the interpretation of results and usefulness of individual methods remain context-dependent.",
journal = "Genome Biology",
title = "An expanded evaluation of protein function prediction methods shows an improvement in accuracy",
volume = "17",
doi = "10.1186/s13059-016-1037-6"
}
Jiang, Y., Gemović, B. S., Glišić, S., Perović, V. R., Veljković, V.,& Veljković, N. V. (2016). An expanded evaluation of protein function prediction methods shows an improvement in accuracy.
Genome Biology, 17.
https://doi.org/10.1186/s13059-016-1037-6
Jiang Y, Gemović BS, Glišić S, Perović VR, Veljković V, Veljković NV. An expanded evaluation of protein function prediction methods shows an improvement in accuracy. Genome Biology. 2016;17
Jiang Yuxiang, Gemović Branislava S., Glišić Sanja, Perović Vladimir R., Veljković Veljko, Veljković Nevena V., "An expanded evaluation of protein function prediction methods shows an improvement in accuracy" Genome Biology, 17 (2016),
https://doi.org/10.1186/s13059-016-1037-6 .
32
238
143
160

Common molecular mechanism of the hepatic lesion and the cardiac parasympathetic regulation in chronic hepatitis C infection: a critical role for the muscarinic receptor type 3

Glišić, Sanja; Cavanaugh, David P.; Chittur, Krishnan K.; Senćanski, Milan V.; Perović, Vladimir R.; Bojić, Tijana

(2016)

TY  - JOUR
AU  - Glišić, Sanja
AU  - Cavanaugh, David P.
AU  - Chittur, Krishnan K.
AU  - Senćanski, Milan V.
AU  - Perović, Vladimir R.
AU  - Bojić, Tijana
PY  - 2016
UR  - http://vinar.vin.bg.ac.rs/handle/123456789/977
AB  - Background: The pathophysiological overlapping between Sjorgens Syndrome (SS) and HCV, presence of anti-muscarinic receptor type 3 (M3R) antibodies in SS, the role that M3R plays in the regulation of the heart rate, has led to the assumption that cardiovagal dysfunction in HCV patients is caused by anti-M3R antibodies elicited by HCV proteins or by their direct interaction with M3R. Results: To identify HCV protein which possibly is crossreactive with M3R or which binds to this receptor, we performed the Informational Spectrum Method (ISM) analysis of the HCV proteome. This analysis revealed that NS5A protein represents the most probable interactor of M3R or that this viral protein could elicit antibodies which modulate function of this receptor. Further detailed structure/function analysis of NS5A and M3R performed by the ISM method extended with other Digital Signal processing (DSP) approaches revealed domains of these proteins which participate in their crossreactivity or in their direct interaction, representing promising diagnostic and therapeutic targets. Conclusions: Application of the ISM with other compatible bioinformatics methods offers new perspectives for identifying diagnostic and therapeutic targets for complicated forms of HCV and other viral infections. We show how the electron-ion interaction potential (EIIP) amino-acid scale used in the ISM combined with a robust, high performance hydrophobicity scale can provide new insights for understanding protein structure/function and protein-protein interactions.
T2  - BMC Bioinformatics
T1  - Common molecular mechanism of the hepatic lesion and the cardiac parasympathetic regulation in chronic hepatitis C infection: a critical role for the muscarinic receptor type 3
VL  - 17
SP  - 139
DO  - 10.1186/s12859-016-0988-7
ER  - 
@article{
author = "Glišić, Sanja and Cavanaugh, David P. and Chittur, Krishnan K. and Senćanski, Milan V. and Perović, Vladimir R. and Bojić, Tijana",
year = "2016",
url = "http://vinar.vin.bg.ac.rs/handle/123456789/977",
abstract = "Background: The pathophysiological overlapping between Sjorgens Syndrome (SS) and HCV, presence of anti-muscarinic receptor type 3 (M3R) antibodies in SS, the role that M3R plays in the regulation of the heart rate, has led to the assumption that cardiovagal dysfunction in HCV patients is caused by anti-M3R antibodies elicited by HCV proteins or by their direct interaction with M3R. Results: To identify HCV protein which possibly is crossreactive with M3R or which binds to this receptor, we performed the Informational Spectrum Method (ISM) analysis of the HCV proteome. This analysis revealed that NS5A protein represents the most probable interactor of M3R or that this viral protein could elicit antibodies which modulate function of this receptor. Further detailed structure/function analysis of NS5A and M3R performed by the ISM method extended with other Digital Signal processing (DSP) approaches revealed domains of these proteins which participate in their crossreactivity or in their direct interaction, representing promising diagnostic and therapeutic targets. Conclusions: Application of the ISM with other compatible bioinformatics methods offers new perspectives for identifying diagnostic and therapeutic targets for complicated forms of HCV and other viral infections. We show how the electron-ion interaction potential (EIIP) amino-acid scale used in the ISM combined with a robust, high performance hydrophobicity scale can provide new insights for understanding protein structure/function and protein-protein interactions.",
journal = "BMC Bioinformatics",
title = "Common molecular mechanism of the hepatic lesion and the cardiac parasympathetic regulation in chronic hepatitis C infection: a critical role for the muscarinic receptor type 3",
volume = "17",
pages = "139",
doi = "10.1186/s12859-016-0988-7"
}
Glišić, S., Cavanaugh, D. P., Chittur, K. K., Senćanski, M. V., Perović, V. R.,& Bojić, T. (2016). Common molecular mechanism of the hepatic lesion and the cardiac parasympathetic regulation in chronic hepatitis C infection: a critical role for the muscarinic receptor type 3.
BMC Bioinformatics, 17, 139.
https://doi.org/10.1186/s12859-016-0988-7
Glišić S, Cavanaugh DP, Chittur KK, Senćanski MV, Perović VR, Bojić T. Common molecular mechanism of the hepatic lesion and the cardiac parasympathetic regulation in chronic hepatitis C infection: a critical role for the muscarinic receptor type 3. BMC Bioinformatics. 2016;17:139
Glišić Sanja, Cavanaugh David P., Chittur Krishnan K., Senćanski Milan V., Perović Vladimir R., Bojić Tijana, "Common molecular mechanism of the hepatic lesion and the cardiac parasympathetic regulation in chronic hepatitis C infection: a critical role for the muscarinic receptor type 3" BMC Bioinformatics, 17 (2016):139,
https://doi.org/10.1186/s12859-016-0988-7 .
4
4
5

In silico Therapeutics for Neurogenic Hypertension and Vasovagal Syncope

Bojić, Tijana; Perović, Vladimir R.; Glišić, Sanja

(2016)

TY  - JOUR
AU  - Bojić, Tijana
AU  - Perović, Vladimir R.
AU  - Glišić, Sanja
PY  - 2016
UR  - http://vinar.vin.bg.ac.rs/handle/123456789/900
AB  - Neurocardiovascular diseases (NCVD) are the leading cause of death in the developed world and will remain so till 2020. In these diseases the pathologically changed nervous control of cardiovascular system has the central role. The actual NCV syndromes are neurogenic hypertension, representing the sympathetically mediated disorder, and vasovagal syncope, which is the vagally mediated disorders. Vasovagal syncope, the disease far from its etiological treatment, could benefit from recruiting and application of antimuscarinic drugs used in other parasympathetic disorders. The informational spectrum method (ISM), a method widely applied for the characterization of protein-protein interactions in the field of immunology, endocrinology and anti HIV drug discovery, was applied for the first time in the analysis of neurogenic hypertension and vasovagal syncope therapeutic targets. In silico analysis revealed the potential involvement of apelin in neurogenic hypertension. Applying the EIIP/ISM bioinformatics concept in investigation of drugs for treatment of vasovagal syncope suggests that 78% of tested antimuscarinic drugs could have anti vasovagal syncope effect. The presented results confirm that ISM is a promissing method for investigation of molecular mechanisms underlying pathophysiological proceses of NCV syndromes and discovery of therapeutics targets for their treatment.
T2  - Frontiers in Neuroscience
T1  - In silico Therapeutics for Neurogenic Hypertension and Vasovagal Syncope
VL  - 9
SP  - 520
DO  - 10.3389/fnins.2015.00520
ER  - 
@article{
author = "Bojić, Tijana and Perović, Vladimir R. and Glišić, Sanja",
year = "2016",
url = "http://vinar.vin.bg.ac.rs/handle/123456789/900",
abstract = "Neurocardiovascular diseases (NCVD) are the leading cause of death in the developed world and will remain so till 2020. In these diseases the pathologically changed nervous control of cardiovascular system has the central role. The actual NCV syndromes are neurogenic hypertension, representing the sympathetically mediated disorder, and vasovagal syncope, which is the vagally mediated disorders. Vasovagal syncope, the disease far from its etiological treatment, could benefit from recruiting and application of antimuscarinic drugs used in other parasympathetic disorders. The informational spectrum method (ISM), a method widely applied for the characterization of protein-protein interactions in the field of immunology, endocrinology and anti HIV drug discovery, was applied for the first time in the analysis of neurogenic hypertension and vasovagal syncope therapeutic targets. In silico analysis revealed the potential involvement of apelin in neurogenic hypertension. Applying the EIIP/ISM bioinformatics concept in investigation of drugs for treatment of vasovagal syncope suggests that 78% of tested antimuscarinic drugs could have anti vasovagal syncope effect. The presented results confirm that ISM is a promissing method for investigation of molecular mechanisms underlying pathophysiological proceses of NCV syndromes and discovery of therapeutics targets for their treatment.",
journal = "Frontiers in Neuroscience",
title = "In silico Therapeutics for Neurogenic Hypertension and Vasovagal Syncope",
volume = "9",
pages = "520",
doi = "10.3389/fnins.2015.00520"
}
Bojić, T., Perović, V. R.,& Glišić, S. (2016). In silico Therapeutics for Neurogenic Hypertension and Vasovagal Syncope.
Frontiers in Neuroscience, 9, 520.
https://doi.org/10.3389/fnins.2015.00520
Bojić T, Perović VR, Glišić S. In silico Therapeutics for Neurogenic Hypertension and Vasovagal Syncope. Frontiers in Neuroscience. 2016;9:520
Bojić Tijana, Perović Vladimir R., Glišić Sanja, "In silico Therapeutics for Neurogenic Hypertension and Vasovagal Syncope" Frontiers in Neuroscience, 9 (2016):520,
https://doi.org/10.3389/fnins.2015.00520 .
2
1
3
3

Arginase Flavonoid Anti-Leishmanial in Silico Inhibitors Flagged against Anti-Targets

Glišić, Sanja; Senćanski, Milan V.; Perović, Vladimir R.; Stevanović, Strahinja; Garcia-Sosa, Alfonso T.

(2016)

TY  - JOUR
AU  - Glišić, Sanja
AU  - Senćanski, Milan V.
AU  - Perović, Vladimir R.
AU  - Stevanović, Strahinja
AU  - Garcia-Sosa, Alfonso T.
PY  - 2016
UR  - http://vinar.vin.bg.ac.rs/handle/123456789/1187
AB  - Arginase, a drug target for the treatment of leishmaniasis, is involved in the biosynthesis of polyamines. Flavonoids are interesting natural compounds found in many foods and some of them may inhibit this enzyme. The MetIDB database containing 5667 compounds was screened using an EIIP/AQVN filter and 3D QSAR to find the most promising candidate compounds. In addition, these top hits were screened in silico versus human arginase and an anti-target battery consisting of cytochromes P450 2a6, 2c9, 3a4, sulfotransferase, and the pregnane-X-receptor in order to flag their possible interactions with these proteins involved in the metabolism of substances. The resulting compounds may have promise to be further developed for the treatment of leishmaniasis.
T2  - Molecules
T1  - Arginase Flavonoid Anti-Leishmanial in Silico Inhibitors Flagged against Anti-Targets
VL  - 21
IS  - 5
DO  - 10.3390/molecules21050589
ER  - 
@article{
author = "Glišić, Sanja and Senćanski, Milan V. and Perović, Vladimir R. and Stevanović, Strahinja and Garcia-Sosa, Alfonso T.",
year = "2016",
url = "http://vinar.vin.bg.ac.rs/handle/123456789/1187",
abstract = "Arginase, a drug target for the treatment of leishmaniasis, is involved in the biosynthesis of polyamines. Flavonoids are interesting natural compounds found in many foods and some of them may inhibit this enzyme. The MetIDB database containing 5667 compounds was screened using an EIIP/AQVN filter and 3D QSAR to find the most promising candidate compounds. In addition, these top hits were screened in silico versus human arginase and an anti-target battery consisting of cytochromes P450 2a6, 2c9, 3a4, sulfotransferase, and the pregnane-X-receptor in order to flag their possible interactions with these proteins involved in the metabolism of substances. The resulting compounds may have promise to be further developed for the treatment of leishmaniasis.",
journal = "Molecules",
title = "Arginase Flavonoid Anti-Leishmanial in Silico Inhibitors Flagged against Anti-Targets",
volume = "21",
number = "5",
doi = "10.3390/molecules21050589"
}
Glišić, S., Senćanski, M. V., Perović, V. R., Stevanović, S.,& Garcia-Sosa, A. T. (2016). Arginase Flavonoid Anti-Leishmanial in Silico Inhibitors Flagged against Anti-Targets.
Molecules, 21(5).
https://doi.org/10.3390/molecules21050589
Glišić S, Senćanski MV, Perović VR, Stevanović S, Garcia-Sosa AT. Arginase Flavonoid Anti-Leishmanial in Silico Inhibitors Flagged against Anti-Targets. Molecules. 2016;21(5)
Glišić Sanja, Senćanski Milan V., Perović Vladimir R., Stevanović Strahinja, Garcia-Sosa Alfonso T., "Arginase Flavonoid Anti-Leishmanial in Silico Inhibitors Flagged against Anti-Targets" Molecules, 21, no. 5 (2016),
https://doi.org/10.3390/molecules21050589 .
16
12
15

Rilmenidine suppresses proliferation and promotes apoptosis via the mitochondrial pathway in human leukemic K562 cells

Srdić-Rajić, Tatjana; Nikolic, Katarina; Cavic, Milena; Đokić, Ivana; Gemović, Branislava S.; Perović, Vladimir R.; Veljković, Nevena V.

(2016)

TY  - JOUR
AU  - Srdić-Rajić, Tatjana
AU  - Nikolic, Katarina
AU  - Cavic, Milena
AU  - Đokić, Ivana
AU  - Gemović, Branislava S.
AU  - Perović, Vladimir R.
AU  - Veljković, Nevena V.
PY  - 2016
UR  - http://vinar.vin.bg.ac.rs/handle/123456789/884
AB  - Imidazoline I1 receptor signaling is associated with pathways that regulate cell viability leading to varied cell-type specific phenotypes. We demonstrated that the antihypertensive drug rilmenidine, a selective imidazoline I1 receptor agonist, modulates proliferation and stimulates the proapoptotic protein Bax thus inducing the perturbation of the mitochondrial pathway and apoptosis in human leukemic K562 cells. Rilmenidine acts through a mechanism which involves deactivation of Ras/MAP kinases ERK, p38 and JNK. Moreover, rilmenidine renders K562 cells, which are particularly resistant to chemotherapeutic agents, susceptible to the DNA damaging drug doxorubicin. The rilmenidine co-treatment with doxorubicin reverses G2/M arrest and triggers apoptotic response to DNA damage. Our data offer new insights into the pathways associated with imidazoline I1 receptor activation in K562 cells suggesting rilmenidine as a valuable tool to deepen our understanding of imidazoline I1 receptor signaling in hematologic malignancies and to search for medicinally active agents. (C) 2015 Elsevier B.V. All rights reserved.
T2  - European Journal of Pharmaceutical Sciences
T1  - Rilmenidine suppresses proliferation and promotes apoptosis via the mitochondrial pathway in human leukemic K562 cells
VL  - 81
SP  - 172
EP  - 180
DO  - 10.1016/j.ejps.2015.10.017
ER  - 
@article{
author = "Srdić-Rajić, Tatjana and Nikolic, Katarina and Cavic, Milena and Đokić, Ivana and Gemović, Branislava S. and Perović, Vladimir R. and Veljković, Nevena V.",
year = "2016",
url = "http://vinar.vin.bg.ac.rs/handle/123456789/884",
abstract = "Imidazoline I1 receptor signaling is associated with pathways that regulate cell viability leading to varied cell-type specific phenotypes. We demonstrated that the antihypertensive drug rilmenidine, a selective imidazoline I1 receptor agonist, modulates proliferation and stimulates the proapoptotic protein Bax thus inducing the perturbation of the mitochondrial pathway and apoptosis in human leukemic K562 cells. Rilmenidine acts through a mechanism which involves deactivation of Ras/MAP kinases ERK, p38 and JNK. Moreover, rilmenidine renders K562 cells, which are particularly resistant to chemotherapeutic agents, susceptible to the DNA damaging drug doxorubicin. The rilmenidine co-treatment with doxorubicin reverses G2/M arrest and triggers apoptotic response to DNA damage. Our data offer new insights into the pathways associated with imidazoline I1 receptor activation in K562 cells suggesting rilmenidine as a valuable tool to deepen our understanding of imidazoline I1 receptor signaling in hematologic malignancies and to search for medicinally active agents. (C) 2015 Elsevier B.V. All rights reserved.",
journal = "European Journal of Pharmaceutical Sciences",
title = "Rilmenidine suppresses proliferation and promotes apoptosis via the mitochondrial pathway in human leukemic K562 cells",
volume = "81",
pages = "172-180",
doi = "10.1016/j.ejps.2015.10.017"
}
Srdić-Rajić, T., Nikolic, K., Cavic, M., Đokić, I., Gemović, B. S., Perović, V. R.,& Veljković, N. V. (2016). Rilmenidine suppresses proliferation and promotes apoptosis via the mitochondrial pathway in human leukemic K562 cells.
European Journal of Pharmaceutical Sciences, 81, 172-180.
https://doi.org/10.1016/j.ejps.2015.10.017
Srdić-Rajić T, Nikolic K, Cavic M, Đokić I, Gemović BS, Perović VR, Veljković NV. Rilmenidine suppresses proliferation and promotes apoptosis via the mitochondrial pathway in human leukemic K562 cells. European Journal of Pharmaceutical Sciences. 2016;81:172-180
Srdić-Rajić Tatjana, Nikolic Katarina, Cavic Milena, Đokić Ivana, Gemović Branislava S., Perović Vladimir R., Veljković Nevena V., "Rilmenidine suppresses proliferation and promotes apoptosis via the mitochondrial pathway in human leukemic K562 cells" European Journal of Pharmaceutical Sciences, 81 (2016):172-180,
https://doi.org/10.1016/j.ejps.2015.10.017 .
7
9
7
9

A combined ligand- and structure-based approach for the identification of rilmenidine-derived compounds which synergize the antitumor effects of doxorubicin

Vucicevic, Jelica; Srdić-Rajić, Tatjana; Pieroni, Marco; Laurila, Jonne M. M.; Perović, Vladimir R.; Tassini, Sabrina; Azzali, Elisa; Costantino, Gabriele; Glišić, Sanja; Agbaba, Danica; Scheinin, Mika; Nikolic, Katarina; Radi, Marco; Veljković, Nevena V.

(2016)

TY  - JOUR
AU  - Vucicevic, Jelica
AU  - Srdić-Rajić, Tatjana
AU  - Pieroni, Marco
AU  - Laurila, Jonne M. M.
AU  - Perović, Vladimir R.
AU  - Tassini, Sabrina
AU  - Azzali, Elisa
AU  - Costantino, Gabriele
AU  - Glišić, Sanja
AU  - Agbaba, Danica
AU  - Scheinin, Mika
AU  - Nikolic, Katarina
AU  - Radi, Marco
AU  - Veljković, Nevena V.
PY  - 2016
UR  - http://vinar.vin.bg.ac.rs/handle/123456789/1110
AB  - The clonidine-like central antihypertensive agent rilmenidine, which has high affinity for I-1-type imidazoline receptors (I-1-IR) was recently found to have cytotoxic effects on cultured cancer cell lines. However, due to its pharmacological effects resulting also from alpha(2)-adrenoceptor activation, rilmenidine cannot be considered a suitable anticancer drug candidate. Here, we report the identification of novel rilmenidine- derived compounds with anticancer potential and devoid of alpha(2)-adrenoceptor effects by means of ligand-and structure-based drug design approaches. Starting from a large virtual library, eleven compounds were selected, synthesized and submitted to biological evaluation. The most active compound 5 exhibited a cytotoxic profile similar to that of rilmenidine, but without appreciable affinity to alpha(2)-adrenoceptors. In addition, compound 5 significantly enhanced the apoptotic response to doxorubicin, and may thus represent an important tool for the development of better adjuvant chemotherapeutic strategies for doxorubicin-insensitive cancers. (C) 2016 Elsevier Ltd. All rights reserved.
T2  - Bioorganic and Medicinal Chemistry
T1  - A combined ligand- and structure-based approach for the identification of rilmenidine-derived compounds which synergize the antitumor effects of doxorubicin
VL  - 24
IS  - 14
SP  - 3174
EP  - 3183
DO  - 10.1016/j.bmc.2016.05.043
ER  - 
@article{
author = "Vucicevic, Jelica and Srdić-Rajić, Tatjana and Pieroni, Marco and Laurila, Jonne M. M. and Perović, Vladimir R. and Tassini, Sabrina and Azzali, Elisa and Costantino, Gabriele and Glišić, Sanja and Agbaba, Danica and Scheinin, Mika and Nikolic, Katarina and Radi, Marco and Veljković, Nevena V.",
year = "2016",
url = "http://vinar.vin.bg.ac.rs/handle/123456789/1110",
abstract = "The clonidine-like central antihypertensive agent rilmenidine, which has high affinity for I-1-type imidazoline receptors (I-1-IR) was recently found to have cytotoxic effects on cultured cancer cell lines. However, due to its pharmacological effects resulting also from alpha(2)-adrenoceptor activation, rilmenidine cannot be considered a suitable anticancer drug candidate. Here, we report the identification of novel rilmenidine- derived compounds with anticancer potential and devoid of alpha(2)-adrenoceptor effects by means of ligand-and structure-based drug design approaches. Starting from a large virtual library, eleven compounds were selected, synthesized and submitted to biological evaluation. The most active compound 5 exhibited a cytotoxic profile similar to that of rilmenidine, but without appreciable affinity to alpha(2)-adrenoceptors. In addition, compound 5 significantly enhanced the apoptotic response to doxorubicin, and may thus represent an important tool for the development of better adjuvant chemotherapeutic strategies for doxorubicin-insensitive cancers. (C) 2016 Elsevier Ltd. All rights reserved.",
journal = "Bioorganic and Medicinal Chemistry",
title = "A combined ligand- and structure-based approach for the identification of rilmenidine-derived compounds which synergize the antitumor effects of doxorubicin",
volume = "24",
number = "14",
pages = "3174-3183",
doi = "10.1016/j.bmc.2016.05.043"
}
Vucicevic, J., Srdić-Rajić, T., Pieroni, M., Laurila, J. M. M., Perović, V. R., Tassini, S., Azzali, E., Costantino, G., Glišić, S., Agbaba, D., Scheinin, M., Nikolic, K., Radi, M.,& Veljković, N. V. (2016). A combined ligand- and structure-based approach for the identification of rilmenidine-derived compounds which synergize the antitumor effects of doxorubicin.
Bioorganic and Medicinal Chemistry, 24(14), 3174-3183.
https://doi.org/10.1016/j.bmc.2016.05.043
Vucicevic J, Srdić-Rajić T, Pieroni M, Laurila JMM, Perović VR, Tassini S, Azzali E, Costantino G, Glišić S, Agbaba D, Scheinin M, Nikolic K, Radi M, Veljković NV. A combined ligand- and structure-based approach for the identification of rilmenidine-derived compounds which synergize the antitumor effects of doxorubicin. Bioorganic and Medicinal Chemistry. 2016;24(14):3174-3183
Vucicevic Jelica, Srdić-Rajić Tatjana, Pieroni Marco, Laurila Jonne M. M., Perović Vladimir R., Tassini Sabrina, Azzali Elisa, Costantino Gabriele, Glišić Sanja, Agbaba Danica, Scheinin Mika, Nikolic Katarina, Radi Marco, Veljković Nevena V., "A combined ligand- and structure-based approach for the identification of rilmenidine-derived compounds which synergize the antitumor effects of doxorubicin" Bioorganic and Medicinal Chemistry, 24, no. 14 (2016):3174-3183,
https://doi.org/10.1016/j.bmc.2016.05.043 .
2
9
10
8

Pomegranate (Punica granatum): a natural source for the development of therapeutic compositions of food supplements with anticancer activities based on electron acceptor molecular characteristics

Veljković, Veljko; Glišić, Sanja; Perović, Vladimir R.; Veljković, Nevena V.; Nicolson, Garth L.

(2016)

TY  - JOUR
AU  - Veljković, Veljko
AU  - Glišić, Sanja
AU  - Perović, Vladimir R.
AU  - Veljković, Nevena V.
AU  - Nicolson, Garth L.
PY  - 2016
UR  - http://vinar.vin.bg.ac.rs/handle/123456789/1372
AB  - Background: Numerous in vitro and in vivo studies, in addition to clinical data, demonstrate that pomegranate juice can prevent or slow-down the progression of some types of cancers. Despite the well-documented effect of pomegranate ingredients on neoplastic changes, the molecular mechanism(s) underlying this phenomenon remains elusive. Methods: For the study of pomegranate ingredients the electron-ion interaction potential (EIIP) and the average quasi valence number (AQVN) were used. These molecular descriptors can be used to describe the long-range intermolecular interactions in biological systems and can identify substances with strong electron-acceptor properties. In this study, candidate human proteins interacting with pomegranate flavonoids have been analyzed by the informational spectrum method (ISM). This represents a virtual spectroscopy method for studying protein molecular interactions. Results: Our analysis indicates that the anti-cancer properties of pomegranate juice can be ascribed to the strong electron-acceptor properties of its chemical ingredients. This analysis also suggests that pomegranate flavonoids inhibit the NF-kappaB (NF-kappa B) pathway, which plays a critical role in the pathogenesis of cancer. Conclusion: The results offer a possible explanation for an important molecular mechanism underlying the anticancer activity of pomegranate ingredients, which could also serve as a basis for the development of new therapeutic compositions of food supplements with pomegranate-like anticancer properties.
T2  - Functional Foods in Health and Disease
T1  - Pomegranate (Punica granatum): a natural source for the development of therapeutic compositions of food supplements with anticancer activities based on electron acceptor molecular characteristics
VL  - 6
IS  - 12
SP  - 769
EP  - 787
ER  - 
@article{
author = "Veljković, Veljko and Glišić, Sanja and Perović, Vladimir R. and Veljković, Nevena V. and Nicolson, Garth L.",
year = "2016",
url = "http://vinar.vin.bg.ac.rs/handle/123456789/1372",
abstract = "Background: Numerous in vitro and in vivo studies, in addition to clinical data, demonstrate that pomegranate juice can prevent or slow-down the progression of some types of cancers. Despite the well-documented effect of pomegranate ingredients on neoplastic changes, the molecular mechanism(s) underlying this phenomenon remains elusive. Methods: For the study of pomegranate ingredients the electron-ion interaction potential (EIIP) and the average quasi valence number (AQVN) were used. These molecular descriptors can be used to describe the long-range intermolecular interactions in biological systems and can identify substances with strong electron-acceptor properties. In this study, candidate human proteins interacting with pomegranate flavonoids have been analyzed by the informational spectrum method (ISM). This represents a virtual spectroscopy method for studying protein molecular interactions. Results: Our analysis indicates that the anti-cancer properties of pomegranate juice can be ascribed to the strong electron-acceptor properties of its chemical ingredients. This analysis also suggests that pomegranate flavonoids inhibit the NF-kappaB (NF-kappa B) pathway, which plays a critical role in the pathogenesis of cancer. Conclusion: The results offer a possible explanation for an important molecular mechanism underlying the anticancer activity of pomegranate ingredients, which could also serve as a basis for the development of new therapeutic compositions of food supplements with pomegranate-like anticancer properties.",
journal = "Functional Foods in Health and Disease",
title = "Pomegranate (Punica granatum): a natural source for the development of therapeutic compositions of food supplements with anticancer activities based on electron acceptor molecular characteristics",
volume = "6",
number = "12",
pages = "769-787"
}
Veljković, V., Glišić, S., Perović, V. R., Veljković, N. V.,& Nicolson, G. L. (2016). Pomegranate (Punica granatum): a natural source for the development of therapeutic compositions of food supplements with anticancer activities based on electron acceptor molecular characteristics.
Functional Foods in Health and Disease, 6(12), 769-787.
Veljković V, Glišić S, Perović VR, Veljković NV, Nicolson GL. Pomegranate (Punica granatum): a natural source for the development of therapeutic compositions of food supplements with anticancer activities based on electron acceptor molecular characteristics. Functional Foods in Health and Disease. 2016;6(12):769-787
Veljković Veljko, Glišić Sanja, Perović Vladimir R., Veljković Nevena V., Nicolson Garth L., "Pomegranate (Punica granatum): a natural source for the development of therapeutic compositions of food supplements with anticancer activities based on electron acceptor molecular characteristics" Functional Foods in Health and Disease, 6, no. 12 (2016):769-787
1

In silico analysis suggests interaction between Ebola virus and the extracellular matrix

Veljković, Veljko; Glišić, Sanja; Muller, Claude P.; Scotch, Matthew; Branch, Donald R.; Perović, Vladimir R.; Senćanski, Milan V.; Veljković, Nevena V.; Colombatti, Alfonso

(2015)

TY  - JOUR
AU  - Veljković, Veljko
AU  - Glišić, Sanja
AU  - Muller, Claude P.
AU  - Scotch, Matthew
AU  - Branch, Donald R.
AU  - Perović, Vladimir R.
AU  - Senćanski, Milan V.
AU  - Veljković, Nevena V.
AU  - Colombatti, Alfonso
PY  - 2015
UR  - http://vinar.vin.bg.ac.rs/handle/123456789/423
AB  - The worst Ebola virus (EV) outbreak in history has hit Liberia, Sierra Leone and Guinea hardest and the trend lines in this crisis are grave, and now represents a global public health threat concern. Limited therapeutic and/or prophylactic options are available for people suffering from Ebola virus disease (EVD) and further complicate the situation. Previous studies suggested that the EV glycoprotein (GP) is the main determinant causing structural damage of endothelial cells that triggers the hemorrhagic diathesis, but molecular mechanisms underlying this phenomenon remains elusive. Using the informational spectrum method (ISM), a virtual spectroscopy method for analysis of the protein-protein interactions, the interaction of GP with endothelial extracellular matrix (ECM) was investigated. Presented results of this in silico study suggest that Elastin Microfibril Interface Located Proteins (EMILINs) are involved in interaction between GP and ECM. This finding could contribute to a better understanding of EV/endothelium interaction and its role in pathogenesis, prevention and therapy of EVD.
T2  - Frontiers in Microbiology
T1  - In silico analysis suggests interaction between Ebola virus and the extracellular matrix
VL  - 6
DO  - 10.3389/fmicb.2015.00135
ER  - 
@article{
author = "Veljković, Veljko and Glišić, Sanja and Muller, Claude P. and Scotch, Matthew and Branch, Donald R. and Perović, Vladimir R. and Senćanski, Milan V. and Veljković, Nevena V. and Colombatti, Alfonso",
year = "2015",
url = "http://vinar.vin.bg.ac.rs/handle/123456789/423",
abstract = "The worst Ebola virus (EV) outbreak in history has hit Liberia, Sierra Leone and Guinea hardest and the trend lines in this crisis are grave, and now represents a global public health threat concern. Limited therapeutic and/or prophylactic options are available for people suffering from Ebola virus disease (EVD) and further complicate the situation. Previous studies suggested that the EV glycoprotein (GP) is the main determinant causing structural damage of endothelial cells that triggers the hemorrhagic diathesis, but molecular mechanisms underlying this phenomenon remains elusive. Using the informational spectrum method (ISM), a virtual spectroscopy method for analysis of the protein-protein interactions, the interaction of GP with endothelial extracellular matrix (ECM) was investigated. Presented results of this in silico study suggest that Elastin Microfibril Interface Located Proteins (EMILINs) are involved in interaction between GP and ECM. This finding could contribute to a better understanding of EV/endothelium interaction and its role in pathogenesis, prevention and therapy of EVD.",
journal = "Frontiers in Microbiology",
title = "In silico analysis suggests interaction between Ebola virus and the extracellular matrix",
volume = "6",
doi = "10.3389/fmicb.2015.00135"
}
Veljković, V., Glišić, S., Muller, C. P., Scotch, M., Branch, D. R., Perović, V. R., Senćanski, M. V., Veljković, N. V.,& Colombatti, A. (2015). In silico analysis suggests interaction between Ebola virus and the extracellular matrix.
Frontiers in Microbiology, 6.
https://doi.org/10.3389/fmicb.2015.00135
Veljković V, Glišić S, Muller CP, Scotch M, Branch DR, Perović VR, Senćanski MV, Veljković NV, Colombatti A. In silico analysis suggests interaction between Ebola virus and the extracellular matrix. Frontiers in Microbiology. 2015;6
Veljković Veljko, Glišić Sanja, Muller Claude P., Scotch Matthew, Branch Donald R., Perović Vladimir R., Senćanski Milan V., Veljković Nevena V., Colombatti Alfonso, "In silico analysis suggests interaction between Ebola virus and the extracellular matrix" Frontiers in Microbiology, 6 (2015),
https://doi.org/10.3389/fmicb.2015.00135 .
2
19
7
11

Natural Products as Promising Therapeutics for Treatment of Influenza Disease

Senćanski, Milan V.; Radosevic, Draginja; Perović, Vladimir R.; Gemović, Branislava S.; Stanojevic, Maja; Veljković, Nevena V.; Glišić, Sanja

(2015)

TY  - JOUR
AU  - Senćanski, Milan V.
AU  - Radosevic, Draginja
AU  - Perović, Vladimir R.
AU  - Gemović, Branislava S.
AU  - Stanojevic, Maja
AU  - Veljković, Nevena V.
AU  - Glišić, Sanja
PY  - 2015
UR  - http://vinar.vin.bg.ac.rs/handle/123456789/806
AB  - The influenza virus represents a permanent global health threat because it circulates not only within but also between numerous host populations, thereby frequently causing unexpected outbreaks in animals and humans with a generally unpredictable course of disease and epidemiology. Conventional influenza therapy is directed against the viral neuraminidase protein, which promotes virus release from infected cells, and the viral ion channel M2, which facilitates viral uncoating. However, these drugs, albeit effective, have a major drawback: their targets are of a highly variable sequence. As a consequence, the virus can readily acquire resistance by mutating the drug targets. Indeed, most seasonal A/H1N1 viruses and the 2009 H1N1 virus are resistant to M2 inhibitors, and a significant proportion of the seasonal A/H1N1 viruses are resistant to the neuraminidase inhibitor oseltamivir. Development of new effective drugs for treatment of disease during the regular influenza seasons and the possible influenza pandemic represents an important goal. The results presented here point out natural products as a promising source of low toxic and widely accessible drug candidates for treatment of the influenza disease. Natural products combined with new therapeutic targets and drug repurposing techniques, which accelerate development of new drugs, serve as an important platform for development of new influenza therapeutics.
T2  - Current Pharmaceutical Design
T1  - Natural Products as Promising Therapeutics for Treatment of Influenza Disease
VL  - 21
IS  - 38
SP  - 5573
EP  - 5588
DO  - 10.2174/1381612821666151002113426
ER  - 
@article{
author = "Senćanski, Milan V. and Radosevic, Draginja and Perović, Vladimir R. and Gemović, Branislava S. and Stanojevic, Maja and Veljković, Nevena V. and Glišić, Sanja",
year = "2015",
url = "http://vinar.vin.bg.ac.rs/handle/123456789/806",
abstract = "The influenza virus represents a permanent global health threat because it circulates not only within but also between numerous host populations, thereby frequently causing unexpected outbreaks in animals and humans with a generally unpredictable course of disease and epidemiology. Conventional influenza therapy is directed against the viral neuraminidase protein, which promotes virus release from infected cells, and the viral ion channel M2, which facilitates viral uncoating. However, these drugs, albeit effective, have a major drawback: their targets are of a highly variable sequence. As a consequence, the virus can readily acquire resistance by mutating the drug targets. Indeed, most seasonal A/H1N1 viruses and the 2009 H1N1 virus are resistant to M2 inhibitors, and a significant proportion of the seasonal A/H1N1 viruses are resistant to the neuraminidase inhibitor oseltamivir. Development of new effective drugs for treatment of disease during the regular influenza seasons and the possible influenza pandemic represents an important goal. The results presented here point out natural products as a promising source of low toxic and widely accessible drug candidates for treatment of the influenza disease. Natural products combined with new therapeutic targets and drug repurposing techniques, which accelerate development of new drugs, serve as an important platform for development of new influenza therapeutics.",
journal = "Current Pharmaceutical Design",
title = "Natural Products as Promising Therapeutics for Treatment of Influenza Disease",
volume = "21",
number = "38",
pages = "5573-5588",
doi = "10.2174/1381612821666151002113426"
}
Senćanski, M. V., Radosevic, D., Perović, V. R., Gemović, B. S., Stanojevic, M., Veljković, N. V.,& Glišić, S. (2015). Natural Products as Promising Therapeutics for Treatment of Influenza Disease.
Current Pharmaceutical Design, 21(38), 5573-5588.
https://doi.org/10.2174/1381612821666151002113426
Senćanski MV, Radosevic D, Perović VR, Gemović BS, Stanojevic M, Veljković NV, Glišić S. Natural Products as Promising Therapeutics for Treatment of Influenza Disease. Current Pharmaceutical Design. 2015;21(38):5573-5588
Senćanski Milan V., Radosevic Draginja, Perović Vladimir R., Gemović Branislava S., Stanojevic Maja, Veljković Nevena V., Glišić Sanja, "Natural Products as Promising Therapeutics for Treatment of Influenza Disease" Current Pharmaceutical Design, 21, no. 38 (2015):5573-5588,
https://doi.org/10.2174/1381612821666151002113426 .
15
15
19

Improving attrition rates in Ebola virus drug discovery

Glišić, Sanja; Paessler, Slobodan; Veljković, Nevena V.; Perović, Vladimir R.; Prljić, Jelena; Veljković, Veljko

(2015)

TY  - JOUR
AU  - Glišić, Sanja
AU  - Paessler, Slobodan
AU  - Veljković, Nevena V.
AU  - Perović, Vladimir R.
AU  - Prljić, Jelena
AU  - Veljković, Veljko
PY  - 2015
UR  - http://vinar.vin.bg.ac.rs/handle/123456789/709
AB  - Introduction: The Ebola 2014/2015 outbreak has had devastating effects on the people living in West Africa. The spread of the disease in endemic countries and the potential introduction of sporadic cases in other continents points out the global health threat of Ebola virus disease (EVD). Despite the urgent need for treating EVD, there are no approved treatments. Given the lack of treatments available, alternative therapeutic strategies have had to be used. Areas covered: This article summarizes the unregistered therapeutics that were used to treat patients during the Ebola 2014/2015 outbreak, in addition to approaches used for the selection of candidate drugs. The article also proposes potential theoretical criterion for use in virtual screening of molecular libraries for candidate Ebola drugs. Expert opinion: In the absence of approved therapeutics for EVD, experimental drugs have had to be used. The repurposing of approved drugs for the treatment of EVD, as an alternative therapeutic strategy, has also been suggested. Screening in vitro- and in sllico-approved drugs revealed several promising candidates but further testing is required to test their efficacy. All these therapeutic approaches are, however, only short-term solutions and there is still an urgent need for the development of specific drugs for the current and future outbreaks.
T2  - Expert Opinion on Drug Discovery
T1  - Improving attrition rates in Ebola virus drug discovery
VL  - 10
IS  - 9
SP  - 1025
EP  - 1032
DO  - 10.1517/17460441.2015.1062872
ER  - 
@article{
author = "Glišić, Sanja and Paessler, Slobodan and Veljković, Nevena V. and Perović, Vladimir R. and Prljić, Jelena and Veljković, Veljko",
year = "2015",
url = "http://vinar.vin.bg.ac.rs/handle/123456789/709",
abstract = "Introduction: The Ebola 2014/2015 outbreak has had devastating effects on the people living in West Africa. The spread of the disease in endemic countries and the potential introduction of sporadic cases in other continents points out the global health threat of Ebola virus disease (EVD). Despite the urgent need for treating EVD, there are no approved treatments. Given the lack of treatments available, alternative therapeutic strategies have had to be used. Areas covered: This article summarizes the unregistered therapeutics that were used to treat patients during the Ebola 2014/2015 outbreak, in addition to approaches used for the selection of candidate drugs. The article also proposes potential theoretical criterion for use in virtual screening of molecular libraries for candidate Ebola drugs. Expert opinion: In the absence of approved therapeutics for EVD, experimental drugs have had to be used. The repurposing of approved drugs for the treatment of EVD, as an alternative therapeutic strategy, has also been suggested. Screening in vitro- and in sllico-approved drugs revealed several promising candidates but further testing is required to test their efficacy. All these therapeutic approaches are, however, only short-term solutions and there is still an urgent need for the development of specific drugs for the current and future outbreaks.",
journal = "Expert Opinion on Drug Discovery",
title = "Improving attrition rates in Ebola virus drug discovery",
volume = "10",
number = "9",
pages = "1025-1032",
doi = "10.1517/17460441.2015.1062872"
}
Glišić, S., Paessler, S., Veljković, N. V., Perović, V. R., Prljić, J.,& Veljković, V. (2015). Improving attrition rates in Ebola virus drug discovery.
Expert Opinion on Drug Discovery, 10(9), 1025-1032.
https://doi.org/10.1517/17460441.2015.1062872
Glišić S, Paessler S, Veljković NV, Perović VR, Prljić J, Veljković V. Improving attrition rates in Ebola virus drug discovery. Expert Opinion on Drug Discovery. 2015;10(9):1025-1032
Glišić Sanja, Paessler Slobodan, Veljković Nevena V., Perović Vladimir R., Prljić Jelena, Veljković Veljko, "Improving attrition rates in Ebola virus drug discovery" Expert Opinion on Drug Discovery, 10, no. 9 (2015):1025-1032,
https://doi.org/10.1517/17460441.2015.1062872 .
2
3
4
5

Evolution of 2014/15 H3N2 Influenza Viruses Circulating in US: Consequences for Vaccine Effectiveness and Possible New Pandemic

Veljković, Veljko; Paessler, Slobodan; Glišić, Sanja; Prljić, Jelena; Perović, Vladimir R.; Veljković, Nevena V.; Scotch, Matthew

(2015)

TY  - JOUR
AU  - Veljković, Veljko
AU  - Paessler, Slobodan
AU  - Glišić, Sanja
AU  - Prljić, Jelena
AU  - Perović, Vladimir R.
AU  - Veljković, Nevena V.
AU  - Scotch, Matthew
PY  - 2015
UR  - http://vinar.vin.bg.ac.rs/handle/123456789/863
AB  - A key factor in the effectiveness of the seasonal influenza vaccine is its immunological compatibility with the circulating viruses during the season. Here we propose a new bioinformatics approach for analysis of influenza viruses which could be used as an efficient tool for selection of vaccine viruses, assessment of the effectiveness of seasonal influenza vaccines, and prediction of the epidemic/pandemic potential of novel influenza viruses.
T2  - Frontiers in Microbiology
T1  - Evolution of 2014/15 H3N2 Influenza Viruses Circulating in US: Consequences for Vaccine Effectiveness and Possible New Pandemic
VL  - 6
DO  - 10.3389/fmicb.2015.01456
ER  - 
@article{
author = "Veljković, Veljko and Paessler, Slobodan and Glišić, Sanja and Prljić, Jelena and Perović, Vladimir R. and Veljković, Nevena V. and Scotch, Matthew",
year = "2015",
url = "http://vinar.vin.bg.ac.rs/handle/123456789/863",
abstract = "A key factor in the effectiveness of the seasonal influenza vaccine is its immunological compatibility with the circulating viruses during the season. Here we propose a new bioinformatics approach for analysis of influenza viruses which could be used as an efficient tool for selection of vaccine viruses, assessment of the effectiveness of seasonal influenza vaccines, and prediction of the epidemic/pandemic potential of novel influenza viruses.",
journal = "Frontiers in Microbiology",
title = "Evolution of 2014/15 H3N2 Influenza Viruses Circulating in US: Consequences for Vaccine Effectiveness and Possible New Pandemic",
volume = "6",
doi = "10.3389/fmicb.2015.01456"
}
Veljković, V., Paessler, S., Glišić, S., Prljić, J., Perović, V. R., Veljković, N. V.,& Scotch, M. (2015). Evolution of 2014/15 H3N2 Influenza Viruses Circulating in US: Consequences for Vaccine Effectiveness and Possible New Pandemic.
Frontiers in Microbiology, 6.
https://doi.org/10.3389/fmicb.2015.01456
Veljković V, Paessler S, Glišić S, Prljić J, Perović VR, Veljković NV, Scotch M. Evolution of 2014/15 H3N2 Influenza Viruses Circulating in US: Consequences for Vaccine Effectiveness and Possible New Pandemic. Frontiers in Microbiology. 2015;6
Veljković Veljko, Paessler Slobodan, Glišić Sanja, Prljić Jelena, Perović Vladimir R., Veljković Nevena V., Scotch Matthew, "Evolution of 2014/15 H3N2 Influenza Viruses Circulating in US: Consequences for Vaccine Effectiveness and Possible New Pandemic" Frontiers in Microbiology, 6 (2015),
https://doi.org/10.3389/fmicb.2015.01456 .
14
11
6
9

Influenza vaccine as prevention for cardiovascular diseases: Possible molecular mechanism

Veljković, Veljko; Glišić, Sanja; Veljković, Nevena V.; Bojić, Tijana; Dietrich, Ursula; Perović, Vladimir R.; Colombatti, Alfonso

(2014)

TY  - JOUR
AU  - Veljković, Veljko
AU  - Glišić, Sanja
AU  - Veljković, Nevena V.
AU  - Bojić, Tijana
AU  - Dietrich, Ursula
AU  - Perović, Vladimir R.
AU  - Colombatti, Alfonso
PY  - 2014
UR  - http://vinar.vin.bg.ac.rs/handle/123456789/229
AB  - Despite plausible evidence for beneficial effects of the vaccination against influenza in cardiovascular diseases (CVD) very limited studies have been carried out to explain the molecular mechanism of this phenomenon. Using the informational spectrum method (ISM), a virtual spectroscopy method for analysis of protein-protein interactions, the bradykinin 2 receptor (BKB2R) was identified as a principal host protein which could mediate molecular processes underlying the cardioprotective effect of influenza vaccines. Based on this finding we suggest that some antibodies elicited by influenza vaccines act as agonists, which activate a BKB2R-associated signaling pathway contributing to the protection against CVD. The ISM analysis of 14 influenza viruses, which were used as components of seasonal vaccines, revealed four vaccine viruses A/Beijing/262/95(H1N1), A/NewCaledonia/20/1999(H1N1), A/Christchurch/28/2003(H3N2) and A/Perth/16/2009(H3N2), which could be suited best for further studies on the cardioprotective effect of influenza vaccines. (C) 2014 Elsevier Ltd. All rights reserved.
T2  - Vaccine
T1  - Influenza vaccine as prevention for cardiovascular diseases: Possible molecular mechanism
VL  - 32
IS  - 48
SP  - 6569
EP  - 6575
DO  - 10.1016/j.vaccine.2014.07.007
ER  - 
@article{
author = "Veljković, Veljko and Glišić, Sanja and Veljković, Nevena V. and Bojić, Tijana and Dietrich, Ursula and Perović, Vladimir R. and Colombatti, Alfonso",
year = "2014",
url = "http://vinar.vin.bg.ac.rs/handle/123456789/229",
abstract = "Despite plausible evidence for beneficial effects of the vaccination against influenza in cardiovascular diseases (CVD) very limited studies have been carried out to explain the molecular mechanism of this phenomenon. Using the informational spectrum method (ISM), a virtual spectroscopy method for analysis of protein-protein interactions, the bradykinin 2 receptor (BKB2R) was identified as a principal host protein which could mediate molecular processes underlying the cardioprotective effect of influenza vaccines. Based on this finding we suggest that some antibodies elicited by influenza vaccines act as agonists, which activate a BKB2R-associated signaling pathway contributing to the protection against CVD. The ISM analysis of 14 influenza viruses, which were used as components of seasonal vaccines, revealed four vaccine viruses A/Beijing/262/95(H1N1), A/NewCaledonia/20/1999(H1N1), A/Christchurch/28/2003(H3N2) and A/Perth/16/2009(H3N2), which could be suited best for further studies on the cardioprotective effect of influenza vaccines. (C) 2014 Elsevier Ltd. All rights reserved.",
journal = "Vaccine",
title = "Influenza vaccine as prevention for cardiovascular diseases: Possible molecular mechanism",
volume = "32",
number = "48",
pages = "6569-6575",
doi = "10.1016/j.vaccine.2014.07.007"
}
Veljković, V., Glišić, S., Veljković, N. V., Bojić, T., Dietrich, U., Perović, V. R.,& Colombatti, A. (2014). Influenza vaccine as prevention for cardiovascular diseases: Possible molecular mechanism.
Vaccine, 32(48), 6569-6575.
https://doi.org/10.1016/j.vaccine.2014.07.007
Veljković V, Glišić S, Veljković NV, Bojić T, Dietrich U, Perović VR, Colombatti A. Influenza vaccine as prevention for cardiovascular diseases: Possible molecular mechanism. Vaccine. 2014;32(48):6569-6575
Veljković Veljko, Glišić Sanja, Veljković Nevena V., Bojić Tijana, Dietrich Ursula, Perović Vladimir R., Colombatti Alfonso, "Influenza vaccine as prevention for cardiovascular diseases: Possible molecular mechanism" Vaccine, 32, no. 48 (2014):6569-6575,
https://doi.org/10.1016/j.vaccine.2014.07.007 .
54
33
29
33

Predicting protein function from sequence and co-expression: preliminary results for breast cancer molecular markers

Gemović, Branislava S.; Perović, Vladimir R.; Glišić, Sanja; Veljković, Nevena V.

(2014)

TY  - CONF
AU  - Gemović, Branislava S.
AU  - Perović, Vladimir R.
AU  - Glišić, Sanja
AU  - Veljković, Nevena V.
PY  - 2014
UR  - http://vinar.vin.bg.ac.rs/handle/123456789/7074
C3  - FEBS Journal
T1  - Predicting protein function from sequence and co-expression: preliminary results for breast cancer molecular markers
VL  - 281
SP  - 633
EP  - 634
ER  - 
@conference{
author = "Gemović, Branislava S. and Perović, Vladimir R. and Glišić, Sanja and Veljković, Nevena V.",
year = "2014",
url = "http://vinar.vin.bg.ac.rs/handle/123456789/7074",
journal = "FEBS Journal",
title = "Predicting protein function from sequence and co-expression: preliminary results for breast cancer molecular markers",
volume = "281",
pages = "633-634"
}
Gemović, B. S., Perović, V. R., Glišić, S.,& Veljković, N. V. (2014). Predicting protein function from sequence and co-expression: preliminary results for breast cancer molecular markers.
FEBS Journal, 281, 633-634.
Gemović BS, Perović VR, Glišić S, Veljković NV. Predicting protein function from sequence and co-expression: preliminary results for breast cancer molecular markers. FEBS Journal. 2014;281:633-634
Gemović Branislava S., Perović Vladimir R., Glišić Sanja, Veljković Nevena V., "Predicting protein function from sequence and co-expression: preliminary results for breast cancer molecular markers" FEBS Journal, 281 (2014):633-634

Novel Phylogenetic Algorithm to Monitor Human Tropism in Egyptian H5N1-HPAIV Reveals Evolution toward Efficient Human-to-Human Transmission

Perović, Vladimir R.; Muller, Claude P.; Niman, Henry L.; Veljković, Nevena V.; Dietrich, Ursula; Tosic, Dusan D.; Glišić, Sanja; Veljković, Veljko

(2013)

TY  - JOUR
AU  - Perović, Vladimir R.
AU  - Muller, Claude P.
AU  - Niman, Henry L.
AU  - Veljković, Nevena V.
AU  - Dietrich, Ursula
AU  - Tosic, Dusan D.
AU  - Glišić, Sanja
AU  - Veljković, Veljko
PY  - 2013
UR  - http://vinar.vin.bg.ac.rs/handle/123456789/5491
AB  - Years of endemic infections with highly pathogenic avian influenza (HPAI) A subtype H5N1 virus in poultry and high numbers of infections in humans provide ample opportunity in Egypt for H5N1-HPAIV to develop pandemic potential. In an effort to better understand the viral determinants that facilitate human infections of the Egyptian H5N1-HPAIVvirus, we developed a new phylogenetic algorithm based on a new distance measure derived from the informational spectrum method (ISM). This new approach, which describes functional aspects of the evolution of the hemagglutinin subunit 1 (HA1), revealed a growing group G2 of H5N1-HPAIV in Egypt after 2009 that acquired new informational spectrum (IS) properties suggestive of an increased human tropism and pandemic potential. While in 2006 all viruses in Egypt belonged to the G1 group, by 2011 these viruses were virtually replaced by G2 viruses. All of the G2 viruses displayed four characteristic mutations (D43N, S120(D,N), (S,L)129 Delta and I151T), three of which were previously reported to increase binding to the human receptor. Already in 2006-2008 G2 viruses were significantly (p LT 0.02) more often found in humans than expected from their overall prevalence and this further increased in 2009-2011 (p LT 0.007). Our approach also identified viruses that acquired additional mutations that we predict to further enhance their human tropism. The extensive evolution of Egyptian H5N1-HPAIV towards a preferential human tropism underlines an urgent need to closely monitor these viruses with respect to molecular determinants of virulence.
T2  - PLOS One
T1  - Novel Phylogenetic Algorithm to Monitor Human Tropism in Egyptian H5N1-HPAIV Reveals Evolution toward Efficient Human-to-Human Transmission
VL  - 8
IS  - 4
DO  - 10.1371/journal.pone.0061572
ER  - 
@article{
author = "Perović, Vladimir R. and Muller, Claude P. and Niman, Henry L. and Veljković, Nevena V. and Dietrich, Ursula and Tosic, Dusan D. and Glišić, Sanja and Veljković, Veljko",
year = "2013",
url = "http://vinar.vin.bg.ac.rs/handle/123456789/5491",
abstract = "Years of endemic infections with highly pathogenic avian influenza (HPAI) A subtype H5N1 virus in poultry and high numbers of infections in humans provide ample opportunity in Egypt for H5N1-HPAIV to develop pandemic potential. In an effort to better understand the viral determinants that facilitate human infections of the Egyptian H5N1-HPAIVvirus, we developed a new phylogenetic algorithm based on a new distance measure derived from the informational spectrum method (ISM). This new approach, which describes functional aspects of the evolution of the hemagglutinin subunit 1 (HA1), revealed a growing group G2 of H5N1-HPAIV in Egypt after 2009 that acquired new informational spectrum (IS) properties suggestive of an increased human tropism and pandemic potential. While in 2006 all viruses in Egypt belonged to the G1 group, by 2011 these viruses were virtually replaced by G2 viruses. All of the G2 viruses displayed four characteristic mutations (D43N, S120(D,N), (S,L)129 Delta and I151T), three of which were previously reported to increase binding to the human receptor. Already in 2006-2008 G2 viruses were significantly (p LT 0.02) more often found in humans than expected from their overall prevalence and this further increased in 2009-2011 (p LT 0.007). Our approach also identified viruses that acquired additional mutations that we predict to further enhance their human tropism. The extensive evolution of Egyptian H5N1-HPAIV towards a preferential human tropism underlines an urgent need to closely monitor these viruses with respect to molecular determinants of virulence.",
journal = "PLOS One",
title = "Novel Phylogenetic Algorithm to Monitor Human Tropism in Egyptian H5N1-HPAIV Reveals Evolution toward Efficient Human-to-Human Transmission",
volume = "8",
number = "4",
doi = "10.1371/journal.pone.0061572"
}
Perović, V. R., Muller, C. P., Niman, H. L., Veljković, N. V., Dietrich, U., Tosic, D. D., Glišić, S.,& Veljković, V. (2013). Novel Phylogenetic Algorithm to Monitor Human Tropism in Egyptian H5N1-HPAIV Reveals Evolution toward Efficient Human-to-Human Transmission.
PLOS One, 8(4).
https://doi.org/10.1371/journal.pone.0061572
Perović VR, Muller CP, Niman HL, Veljković NV, Dietrich U, Tosic DD, Glišić S, Veljković V. Novel Phylogenetic Algorithm to Monitor Human Tropism in Egyptian H5N1-HPAIV Reveals Evolution toward Efficient Human-to-Human Transmission. PLOS One. 2013;8(4)
Perović Vladimir R., Muller Claude P., Niman Henry L., Veljković Nevena V., Dietrich Ursula, Tosic Dusan D., Glišić Sanja, Veljković Veljko, "Novel Phylogenetic Algorithm to Monitor Human Tropism in Egyptian H5N1-HPAIV Reveals Evolution toward Efficient Human-to-Human Transmission" PLOS One, 8, no. 4 (2013),
https://doi.org/10.1371/journal.pone.0061572 .
27
19
23

Razvoj multifunkcionalne bioinformatičkeplatforme zasnovane na potencijalu elektron-jon interakcije bioloških molekula

Perović, Vladimir R.

(Универзитет у Београду, Математички факултет, 2013)

TY  - BOOK
AU  - Perović, Vladimir R.
PY  - 2013
UR  - http://eteze.bg.ac.rs/application/showtheses?thesesId=3626
UR  - https://fedorabg.bg.ac.rs/fedora/get/o:12399/bdef:Content/download
UR  - http://vbs.rs/scripts/cobiss?command=DISPLAY&base=70036&RID=45437711
UR  - http://nardus.mpn.gov.rs/123456789/6498
UR  - http://vinar.vin.bg.ac.rs/handle/123456789/7303
AB  - Iako dalekodoseţne međumolekulske interakcije (interakcije na rastojanjima >5Å) igraju značajnu ulogu u prepoznavanju i selektivnom međusobnom privlačenju molekula u biološkim sistemima, do sada nije razvijen odgovarajući softverski paket koji bi omogućio da se ova vaţna osobina uključi u izučavanje biološki aktivnih molekula. U ovom radu je razvijena multifunkcionalna softverska EIIP/ISM platforma zasnovana na fizičkim parametrima organskih molekula koji definišu njihovu dalekodoseţnu interakciju. Ova platforma omogućava (i) izučavanje protein-protein interakcije i interakcije između proteina i malih molekula, (ii) izučavanje veze izmeĎu strukture i funkcije proteina, (iii) procenu uticaja mutacija na biološku funkciju proteina, (iv) praćenje funkcionalne evolucije proteina, (v) dizajniranje molekula ţeljene biološke aktivnosti i (vi) selekciju potencijalnih terapeutskih molekula. Rezultati primene EIIP/ISM platforme na različite konkretne probleme kao što su evolucija virusa gripa, analiza mutacija na LPL proteinu koje predstavljaju faktor rizika za nastanak kardiovaskularnih bolesti, identifikacija terapeutskih targeta za viruse HIV-1 i viruse gripa, selekcija kandidata za antibiotike i lekove za SIDU virtuelnim pretraţivanjem molekulskih biblioteka, koji su prikazani u ovom radu, potvrdili su primenjivost ove platforme u rešavanju širokog spektra problema u molekularnoj biologiji, biomedicini i farmaciji.
AB  - Although long-range intermolecular interactions (interactions acting on distances >5Å) play an important role in recognition and targeting between molecules in biological systems, there is no one appropriate software package allowing use of this important property in investigation of biologically active molecules. The multifunctional EIIP/ISM software, which is based on physical parameters determining long-range molecular properties, was developed in this thesis. This novel and unique platform allows (i) investigation of protein-protein and protein-small molecule interactions, (ii) analysis of structure/function relationship of proteins, (iii) assessment of biological effects of mutations in proteins, (iv) monitoring of the functional evolution of proteins, (v) ―de novo‖ design of molecules with desired biological function and (vi) selection of candidate therapeutic molecules. Results of application of the EIIP/ISM platform on diverse problems (e.g. the evolution of influenza A viruses, assessment of biological effects of mutations on the LPL protein, representing a risk factor for cardiovascular diseases, identification of therapeutic targets for HIV and influenza viruses, virtual screening of molecular libraries for candidate antibiotics and anti-HIV drugs) which are presented in this thesis, confirm the applicability of this platform on broad spectrum of problems in molecular biology, biomedicine and pharmacology.
PB  - Универзитет у Београду, Математички факултет
T2  - Универзитет у Београду
T1  - Razvoj multifunkcionalne bioinformatičkeplatforme zasnovane na potencijalu elektron-jon interakcije bioloških molekula
T1  - Development of multifunctional bioinformaticsplatform based on electron-ion interaction potential of biological molecules
ER  - 
@phdthesis{
author = "Perović, Vladimir R.",
year = "2013",
url = "http://eteze.bg.ac.rs/application/showtheses?thesesId=3626, https://fedorabg.bg.ac.rs/fedora/get/o:12399/bdef:Content/download, http://vbs.rs/scripts/cobiss?command=DISPLAY&base=70036&RID=45437711, http://nardus.mpn.gov.rs/123456789/6498, http://vinar.vin.bg.ac.rs/handle/123456789/7303",
abstract = "Iako dalekodoseţne međumolekulske interakcije (interakcije na rastojanjima >5Å) igraju značajnu ulogu u prepoznavanju i selektivnom međusobnom privlačenju molekula u biološkim sistemima, do sada nije razvijen odgovarajući softverski paket koji bi omogućio da se ova vaţna osobina uključi u izučavanje biološki aktivnih molekula. U ovom radu je razvijena multifunkcionalna softverska EIIP/ISM platforma zasnovana na fizičkim parametrima organskih molekula koji definišu njihovu dalekodoseţnu interakciju. Ova platforma omogućava (i) izučavanje protein-protein interakcije i interakcije između proteina i malih molekula, (ii) izučavanje veze izmeĎu strukture i funkcije proteina, (iii) procenu uticaja mutacija na biološku funkciju proteina, (iv) praćenje funkcionalne evolucije proteina, (v) dizajniranje molekula ţeljene biološke aktivnosti i (vi) selekciju potencijalnih terapeutskih molekula. Rezultati primene EIIP/ISM platforme na različite konkretne probleme kao što su evolucija virusa gripa, analiza mutacija na LPL proteinu koje predstavljaju faktor rizika za nastanak kardiovaskularnih bolesti, identifikacija terapeutskih targeta za viruse HIV-1 i viruse gripa, selekcija kandidata za antibiotike i lekove za SIDU virtuelnim pretraţivanjem molekulskih biblioteka, koji su prikazani u ovom radu, potvrdili su primenjivost ove platforme u rešavanju širokog spektra problema u molekularnoj biologiji, biomedicini i farmaciji., Although long-range intermolecular interactions (interactions acting on distances >5Å) play an important role in recognition and targeting between molecules in biological systems, there is no one appropriate software package allowing use of this important property in investigation of biologically active molecules. The multifunctional EIIP/ISM software, which is based on physical parameters determining long-range molecular properties, was developed in this thesis. This novel and unique platform allows (i) investigation of protein-protein and protein-small molecule interactions, (ii) analysis of structure/function relationship of proteins, (iii) assessment of biological effects of mutations in proteins, (iv) monitoring of the functional evolution of proteins, (v) ―de novo‖ design of molecules with desired biological function and (vi) selection of candidate therapeutic molecules. Results of application of the EIIP/ISM platform on diverse problems (e.g. the evolution of influenza A viruses, assessment of biological effects of mutations on the LPL protein, representing a risk factor for cardiovascular diseases, identification of therapeutic targets for HIV and influenza viruses, virtual screening of molecular libraries for candidate antibiotics and anti-HIV drugs) which are presented in this thesis, confirm the applicability of this platform on broad spectrum of problems in molecular biology, biomedicine and pharmacology.",
publisher = "Универзитет у Београду, Математички факултет",
journal = "Универзитет у Београду",
title = "Razvoj multifunkcionalne bioinformatičkeplatforme zasnovane na potencijalu elektron-jon interakcije bioloških molekula, Development of multifunctional bioinformaticsplatform based on electron-ion interaction potential of biological molecules"
}
Perović, V. R. (2013). Development of multifunctional bioinformaticsplatform based on electron-ion interaction potential of biological molecules.
Универзитет у Београду
Универзитет у Београду, Математички факултет..
Perović VR. Development of multifunctional bioinformaticsplatform based on electron-ion interaction potential of biological molecules. Универзитет у Београду. 2013;
Perović Vladimir R., "Development of multifunctional bioinformaticsplatform based on electron-ion interaction potential of biological molecules" Универзитет у Београду (2013)