TY  - JOUR
AU  - Vojisavljevic, V.
AU  - Pirogova, E.
AU  - Davidović, Dragomir M.
AU  - Cosic, I.
PY  - 2011
UR  - https://vinar.vin.bg.ac.rs/handle/123456789/4226
AB  - A number of biotechnology applications are based on protein design. For this design, the relationship between a proteins primary structure and its conformation is of vital importance. A beta-sheet is a common feature of a proteins two-dimensional structure; therefore, elucidating the principles governing beta-sheet structure and its stability is critical for understanding the protein-folding process. In the three-dimensional representation of protein molecules, C(alpha) carbon coordinates (carbon atom immediately adjacent to the carboxylate group) have often been employed instead of the complete set of coordinates for the corresponding residues. Using the C(alpha) carbon coordinates, we showed that particular amino acids are not randomly distributed within a beta-sheet structure. On the basis of a new statistical approach for the analysis of a spatial distribution of amino acids in a protein, presented by their physico-chemical parameters, the electron-ion interaction potential (EIIP) and hydrophobicity, are described here. The relationship between amino acid positions inside the beta-sheet and the EIIP and hydrophobicity parameters was established. The correlation between amino acid propensities related to the beta-sheet was examined using multiple cross-spectra analysis. We also applied the continuous wavelet transform for the analysis of selected beta-sheet structures using the EIIP and hydrophobicity parameters. The findings provide new insight into conformational propensities of amino acids for the adaption of beta-sheet structures.
T2  - Proceedings of the Royal Society. A: Mathematical, Physical and Engineering Sciences
T1  - Hybrid approach to analysis of beta-sheet structures based on signal processing and statistical consideration
VL  - 467
IS  - 2128
SP  - 1052
EP  - 1072
DO  - 10.1098/rspa.2010.0382
ER  - 

@article{
author = "Vojisavljevic, V. and Pirogova, E. and Davidović, Dragomir M. and Cosic, I.",
year = "2011",
abstract = "A number of biotechnology applications are based on protein design. For this design, the relationship between a proteins primary structure and its conformation is of vital importance. A beta-sheet is a common feature of a proteins two-dimensional structure; therefore, elucidating the principles governing beta-sheet structure and its stability is critical for understanding the protein-folding process. In the three-dimensional representation of protein molecules, C(alpha) carbon coordinates (carbon atom immediately adjacent to the carboxylate group) have often been employed instead of the complete set of coordinates for the corresponding residues. Using the C(alpha) carbon coordinates, we showed that particular amino acids are not randomly distributed within a beta-sheet structure. On the basis of a new statistical approach for the analysis of a spatial distribution of amino acids in a protein, presented by their physico-chemical parameters, the electron-ion interaction potential (EIIP) and hydrophobicity, are described here. The relationship between amino acid positions inside the beta-sheet and the EIIP and hydrophobicity parameters was established. The correlation between amino acid propensities related to the beta-sheet was examined using multiple cross-spectra analysis. We also applied the continuous wavelet transform for the analysis of selected beta-sheet structures using the EIIP and hydrophobicity parameters. The findings provide new insight into conformational propensities of amino acids for the adaption of beta-sheet structures.",
journal = "Proceedings of the Royal Society. A: Mathematical, Physical and Engineering Sciences",
title = "Hybrid approach to analysis of beta-sheet structures based on signal processing and statistical consideration",
volume = "467",
number = "2128",
pages = "1052-1072",
doi = "10.1098/rspa.2010.0382"
}

Vojisavljevic, V., Pirogova, E., Davidović, D. M.,& Cosic, I.. (2011). Hybrid approach to analysis of beta-sheet structures based on signal processing and statistical consideration. in Proceedings of the Royal Society. A: Mathematical, Physical and Engineering Sciences, 467(2128), 1052-1072.
https://doi.org/10.1098/rspa.2010.0382

Vojisavljevic V, Pirogova E, Davidović DM, Cosic I. Hybrid approach to analysis of beta-sheet structures based on signal processing and statistical consideration. in Proceedings of the Royal Society. A: Mathematical, Physical and Engineering Sciences. 2011;467(2128):1052-1072.
doi:10.1098/rspa.2010.0382 .

Vojisavljevic, V., Pirogova, E., Davidović, Dragomir M., Cosic, I., "Hybrid approach to analysis of beta-sheet structures based on signal processing and statistical consideration" in Proceedings of the Royal Society. A: Mathematical, Physical and Engineering Sciences, 467, no. 2128 (2011):1052-1072,
https://doi.org/10.1098/rspa.2010.0382 . .

TY  - JOUR
AU  - Keković, Goran
AU  - Raković, Dejan
AU  - Tosic, B.
AU  - Davidović, David
AU  - Cosic, I.
PY  - 2010
UR  - https://vinar.vin.bg.ac.rs/handle/123456789/6869
AB  - Biomolecular recognition is an open scientific problem, which has been investigated in many theoretical and experimental aspects. In that sense, there are encouraging results within Resonant Recognition Model (RRM), based on the finding that there is a significant correlation between spectra of the numerical presentation of amino acids in the primary structure of proteins and their biological activity. It has been found through an extensive research that proteins with the same biological function have a common frequency in their numerical spectra. This frequency was found then to be a characteristic feature for protein biological function or interaction The RRM model proposes that the selectivity of protein interactions is based on resonant energy transfer between interacting biomolecules and that this energy, electromagnetic in its nature, is in the frequency range of 10(13) to 10(15) Hz, which incorporates infra-red (IR), visible and a small portion of the ultra-violet (UV) radiation. In this paper, the quantum mechanical basis of the RRM model will be investigated using the solution in the simplified framework of Huckel-like theory of molecular orbits.
T2  - Acta Physica Polonica A
T1  - Quantum Foundations of Resonant Recognition Model
VL  - 117
IS  - 5
SP  - 756
EP  - 759
DO  - 10.12693/APhysPolA.117.756
ER  - 

@article{
author = "Keković, Goran and Raković, Dejan and Tosic, B. and Davidović, David and Cosic, I.",
year = "2010",
abstract = "Biomolecular recognition is an open scientific problem, which has been investigated in many theoretical and experimental aspects. In that sense, there are encouraging results within Resonant Recognition Model (RRM), based on the finding that there is a significant correlation between spectra of the numerical presentation of amino acids in the primary structure of proteins and their biological activity. It has been found through an extensive research that proteins with the same biological function have a common frequency in their numerical spectra. This frequency was found then to be a characteristic feature for protein biological function or interaction The RRM model proposes that the selectivity of protein interactions is based on resonant energy transfer between interacting biomolecules and that this energy, electromagnetic in its nature, is in the frequency range of 10(13) to 10(15) Hz, which incorporates infra-red (IR), visible and a small portion of the ultra-violet (UV) radiation. In this paper, the quantum mechanical basis of the RRM model will be investigated using the solution in the simplified framework of Huckel-like theory of molecular orbits.",
journal = "Acta Physica Polonica A",
title = "Quantum Foundations of Resonant Recognition Model",
volume = "117",
number = "5",
pages = "756-759",
doi = "10.12693/APhysPolA.117.756"
}

Keković, G., Raković, D., Tosic, B., Davidović, D.,& Cosic, I.. (2010). Quantum Foundations of Resonant Recognition Model. in Acta Physica Polonica A, 117(5), 756-759.
https://doi.org/10.12693/APhysPolA.117.756

Keković G, Raković D, Tosic B, Davidović D, Cosic I. Quantum Foundations of Resonant Recognition Model. in Acta Physica Polonica A. 2010;117(5):756-759.
doi:10.12693/APhysPolA.117.756 .

Keković, Goran, Raković, Dejan, Tosic, B., Davidović, David, Cosic, I., "Quantum Foundations of Resonant Recognition Model" in Acta Physica Polonica A, 117, no. 5 (2010):756-759,
https://doi.org/10.12693/APhysPolA.117.756 . .

TY  - CONF
AU  - Vojisavljevic, Vuk
AU  - Pirogova, Elena
AU  - Davidović, Dragomir
AU  - Cosic, Irena
PY  - 2009
UR  - https://vinar.vin.bg.ac.rs/handle/123456789/6883
AB  - A proteins biological function is encrypted within its primary structure. Nevertheless, revealing protein function from analysis of its primary structure is still unsolved problem. In this article we present a new methodology for determining functionally significant amino acid residues in proteins sequences, which is based on time-frequency signal analysis and Smoothed Pseudo Wigner Ville distribution (SPWV). This investigation is the extension of the Resonant Recognition Model (RRM) approach designed for structure-function analysis of proteins and DNA. The RRM is based on the finding that there is a significant correlation between spectra of the numerical presentation of amino acids and their biological activity. The RRM assumes that the selectivity of protein interactions is based on the resonant electromagnetic energy transfer at the specific frequency for each interaction. In this study Cytochrome C, Glucagon, and Hemoglobin proteins were used as the protein examples. By incorporating the SPWV distribution in the RRM, we can define the active regions along the protein molecule. In addition, it was also shown that our computational predictions are corresponding closely with the experimentally identified locations of the active/binding sites for the selected protein examples.
T1  - A new Approach to Revealing Functional Residues from Analysis of Protein Primary Structure
SP  - 4731
EP  - +
DO  - 10.1109/IEMBS.2009.5334193
ER  - 

@conference{
author = "Vojisavljevic, Vuk and Pirogova, Elena and Davidović, Dragomir and Cosic, Irena",
year = "2009",
abstract = "A proteins biological function is encrypted within its primary structure. Nevertheless, revealing protein function from analysis of its primary structure is still unsolved problem. In this article we present a new methodology for determining functionally significant amino acid residues in proteins sequences, which is based on time-frequency signal analysis and Smoothed Pseudo Wigner Ville distribution (SPWV). This investigation is the extension of the Resonant Recognition Model (RRM) approach designed for structure-function analysis of proteins and DNA. The RRM is based on the finding that there is a significant correlation between spectra of the numerical presentation of amino acids and their biological activity. The RRM assumes that the selectivity of protein interactions is based on the resonant electromagnetic energy transfer at the specific frequency for each interaction. In this study Cytochrome C, Glucagon, and Hemoglobin proteins were used as the protein examples. By incorporating the SPWV distribution in the RRM, we can define the active regions along the protein molecule. In addition, it was also shown that our computational predictions are corresponding closely with the experimentally identified locations of the active/binding sites for the selected protein examples.",
title = "A new Approach to Revealing Functional Residues from Analysis of Protein Primary Structure",
pages = "4731-+",
doi = "10.1109/IEMBS.2009.5334193"
}

Vojisavljevic, V., Pirogova, E., Davidović, D.,& Cosic, I.. (2009). A new Approach to Revealing Functional Residues from Analysis of Protein Primary Structure. , 4731-+.
https://doi.org/10.1109/IEMBS.2009.5334193

Vojisavljevic V, Pirogova E, Davidović D, Cosic I. A new Approach to Revealing Functional Residues from Analysis of Protein Primary Structure. 2009;:4731-+.
doi:10.1109/IEMBS.2009.5334193 .

Vojisavljevic, Vuk, Pirogova, Elena, Davidović, Dragomir, Cosic, Irena, "A new Approach to Revealing Functional Residues from Analysis of Protein Primary Structure" (2009):4731-+,
https://doi.org/10.1109/IEMBS.2009.5334193 . .

TY  - JOUR
AU  - Raković, Dejan
AU  - Dugic, M.
AU  - Plavsic, M.
AU  - Keković, Goran
AU  - Cosic, I.
AU  - Davidovic, D.
PY  - 2006
UR  - https://vinar.vin.bg.ac.rs/handle/123456789/6616
AB  - Our recently proposed quantum approach to biomolecular recognition processes is hereby additionally supported by biomolecular Resonant Recognition Model and by quantum-chemical theory of biomolecular non-radiative resonant transitions. Previously developed general quantum-decoherence framework for biopolymer conformational changes in very selective ligand-proteins/target-receptors key/lock biomolecular recognition processes (with electron-conformational coupling, giving rise to dynamical modification of many-electron energy-state hypersurface of the cellular quantum-ensemble ligand-proteins/target-receptors biomolecular macroscopic quantum system, with revealed possibility to consider cellular biomolecular recognition as a Hopfield-like quantum-holographic associative neural network) is further extended from nonlocal macroscopic-quantum level of biological cell to nonlocal macroscopic-quantum level of biological organism, based on long-range coherent microwave excitations (as supported by macroscopic quantum-like microwave resonance therapy of the acupuncture system) - which might be of fundamental importance in understanding of underlying macroscopic quantum (quantum-holographic Hopfield-like) control mechanisms of embryogenesis/ontogenesis and morphogenesis, and their backward influence on the expression of genes.
T2  - Materials Science Forum
T1  - Quantum decoherence and quantum-holographic information processes: From biomolecules to biosystems
VL  - 518
SP  - 485
EP  - 490
DO  - 10.4028/www.scientific.net/MSF.518.485
ER  - 

@article{
author = "Raković, Dejan and Dugic, M. and Plavsic, M. and Keković, Goran and Cosic, I. and Davidovic, D.",
year = "2006",
abstract = "Our recently proposed quantum approach to biomolecular recognition processes is hereby additionally supported by biomolecular Resonant Recognition Model and by quantum-chemical theory of biomolecular non-radiative resonant transitions. Previously developed general quantum-decoherence framework for biopolymer conformational changes in very selective ligand-proteins/target-receptors key/lock biomolecular recognition processes (with electron-conformational coupling, giving rise to dynamical modification of many-electron energy-state hypersurface of the cellular quantum-ensemble ligand-proteins/target-receptors biomolecular macroscopic quantum system, with revealed possibility to consider cellular biomolecular recognition as a Hopfield-like quantum-holographic associative neural network) is further extended from nonlocal macroscopic-quantum level of biological cell to nonlocal macroscopic-quantum level of biological organism, based on long-range coherent microwave excitations (as supported by macroscopic quantum-like microwave resonance therapy of the acupuncture system) - which might be of fundamental importance in understanding of underlying macroscopic quantum (quantum-holographic Hopfield-like) control mechanisms of embryogenesis/ontogenesis and morphogenesis, and their backward influence on the expression of genes.",
journal = "Materials Science Forum",
title = "Quantum decoherence and quantum-holographic information processes: From biomolecules to biosystems",
volume = "518",
pages = "485-490",
doi = "10.4028/www.scientific.net/MSF.518.485"
}

Raković, D., Dugic, M., Plavsic, M., Keković, G., Cosic, I.,& Davidovic, D.. (2006). Quantum decoherence and quantum-holographic information processes: From biomolecules to biosystems. in Materials Science Forum, 518, 485-490.
https://doi.org/10.4028/www.scientific.net/MSF.518.485

Raković D, Dugic M, Plavsic M, Keković G, Cosic I, Davidovic D. Quantum decoherence and quantum-holographic information processes: From biomolecules to biosystems. in Materials Science Forum. 2006;518:485-490.
doi:10.4028/www.scientific.net/MSF.518.485 .

Raković, Dejan, Dugic, M., Plavsic, M., Keković, Goran, Cosic, I., Davidovic, D., "Quantum decoherence and quantum-holographic information processes: From biomolecules to biosystems" in Materials Science Forum, 518 (2006):485-490,
https://doi.org/10.4028/www.scientific.net/MSF.518.485 . .