Timofey V. Pyrkov

Ph.D. (physico-mathematical sciences)

E-mail: tim.pyrkov@gmail.com

Selected publications

  1. Pyrkov T.V., Chugunov A.O., Krylov N.A., Nolde D.E., Efremov R.G. (2009). PLATINUM: a web tool for analysis of hydrophobic/hydrophilic organization of biomolecular complexes. Bioinformatics 25 (9), 1201–2 [+]

    The PLATINUM (Protein-Ligand ATtractions Investigation NUMerically) web service is designed for analysis and visualization of hydrophobic/hydrophilic properties of biomolecules supplied as 3D-structures. Furthermore, PLATINUM provides a number of tools for quantitative characterization of the hydrophobic/hydrophilic match in biomolecular complexes e.g. in docking poses. These complement standard scoring functions. The calculations are based on the concept of empirical Molecular Hydrophobicity Potential (MHP). AVAILABILITY: The PLATINUM web tool as well as detailed documentation and tutorial are available free of charge for academic users at http://model.nmr.ru/platinum/. PLATINUM requires Java 5 or higher and Adobe Flash Player 9. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

  2. Pyrkov T.V., Kosinsky Y.A., Arseniev A.S., Priestle J.P., Jacoby E., Efremov R.G. (2007). Complementarity of hydrophobic properties in ATP-protein binding: a new criterion to rank docking solutions. Proteins 66 (2), 388–98 [+]

    Analysis of X-ray structures of ATP-protein complexes was carried out to reveal the major determinants of adenin recognition by proteins. We demonstrated that hydrophobic contacts and stacking play the main role here. Efficient adenin-specific scoring function was proposed to filter the results of molecular docking.

  3. Efremov R.G., Chugunov A.O., Pyrkov T.V., Priestle J.P., Arseniev A.S., Jacoby E. (2007). Molecular lipophilicity in protein modeling and drug design. Curr. Med. Chem. 14 (4), 393–415 [+]

    Hydrophobic interactions play a key role in the folding and maintenance of the 3-dimensional structure of proteins, as well as in the binding of ligands (e.g. drugs) to protein targets. Therefore, quantitative assessment of spatial hydrophobic (lipophilic) properties of these molecules is indispensable for the development of efficient computational methods in drug design. One possible solution to the problem lies in application of a concept of the 3-dimensional molecular hydrophobicity potential (MHP). The formalism of MHP utilizes a set of atomic physicochemical parameters evaluated from octanol-water partition coefficients (log P) of numerous chemical compounds. It permits detailed assessment of the hydrophobic and/or hydrophilic properties of various parts of molecules and may be useful in analysis of protein-protein and protein-ligand interactions. This review surveys recent applications of MHP-based techniques to a number of biologically relevant tasks. Among them are: (i) Detailed assessment of hydrophobic/hydrophilic organization of proteins; (ii) Application of this data to the modeling of structure, dynamics, and function of globular and membrane proteins, membrane-active peptides, etc. (iii) Employment of the MHP-based criteria in docking simulations for ligands binding to receptors. It is demonstrated that the application of the MHP-based techniques in combination with other molecular modeling tools (e.g. Monte Carlo and molecular dynamics simulations, docking, etc.) permits significant improvement to the standard computational approaches, provides additional important insights into the intimate molecular mechanisms driving protein assembling in water and in biological membranes, and helps in the computer-aided drug discovery process.