Abstract
Molecular docking is one of the most common and popular computational methods in structural biology. It is widely used for investigations of molecular details of protein functioning and in drug design. Nevertheless, modern docking algorithms are still far from perfection. Development of scoring functions aimed at prediction of spatial structure and free energy of binding for molecular complexes remains a challenging task. With increasing amount of structural data, creation of precise system-specific scoring functions becomes possible. This article describes the physical phenomena underlying efficiency of such scoring functions and demonstrates the related quantitative approaches by the examples of guanine-containing ligands and thrombin.
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References
Zhong H, Tran LM, Stang JL (2009) Induced-fit docking studies of the active and inactive states of protein tyrosine kinases. J Mol Graph Model 28:558–575
Kokh DB, Wenzel W (2008) Flexible side chain models improve enrichment rates in in silico screening. J Med Chem 51:5919–5931
Pyrkov TV, Chugunov AO, Krylov NA, Nolde DE, Efremov RG (2009) Complementarity of hydrophobic/hydrophilic properties in protein-ligand complexes. In: Joseph D (ed) A new tool to improve docking results, Biophysics and the challenges of emerging threats, Puglisi, pp 21–41
Rognan D, Lauemoller SL, Holm A, Buus S, Tschinke V (1999) Predicting binding affinities of protein ligands from three-dimensional models: application to peptide binding to class I major histocompatibility proteins. J Med Chem 42:4650–4658
Laederach A, Reilly PJ (2005) Modeling protein recognition of carbohydrates. Proteins 60: 591–597
Pyrkov TV, Kosinsky YA, Arseniev AS, Priestle JP, Jacoby E, Efremov RG (2007) Complementarity of hydrophobic properties in ATP-protein binding: a new criterion to rank docking solutions. Proteins 66:388–398
Pyrkov TV, Ozerov IV, Blitskaia ED, Efremov RG (2010) Molecular docking: role of intermolecular contacts in formation of complexes of proteins with nucleotides and peptides. Bioorg Khim 36:482–492
Gotoh O (1983) Prediction of melting profiles and local helix stability for sequenced DNA. Adv Biophys 16:1–52
Sponer J, Leszczynski J, Hobza P (1996) Hydrogen bonding and stacking of DNA bases: a review of quantum-chemical ab initio studies. J Biomol Struct Dynam 14:117–135
Jorgensen WL, Severance DL (1990) Aromatic-aromatic interactions: free energy profiles for the benzene dimer in water, chloroform, and liquid benzene. J Am Chem Soc 112:4768–4774
Waters ML (2002) Aromatic interactions in model systems. Curr Opin Chem Biol 6:736–741
Meyer EA, Castellano RK, Diederich F (2003) Interactions with aromatic rings in chemical and biological recognition. Angew Chem Int Ed 42:1210–1250
Tewari AK, Dubey R (2008) Emerging trends in molecular recognition: utility of weak aromatic interactions. Bioorg Med Chem 16:126–143
Efremov RG, Chugunov AO, Pyrkov TV, Priestle JP, Arseniev AS, Jacoby E (2007) Molecular lipophilicity in protein modeling and drug design. Curr Med Chem 14:393–415
Pyrkov TV, Priestle JP, Jacoby E, Efremov RG (2008) Ligand-specific scoring functions: improved ranking of docking solutions. SAR QSAR Environ Res 19:91–99
Novoseletsky VN, Pyrkov TV, Efremov RG (2010) Analysis of hydrophobic interactions of antagonists with the beta2-adrenergic receptor. SAR QSAR Environ Res 21:37–55
Fauchere JL, Quarendon P, Kaetterer L (1988) Estimating and representing hydrophobicity potential. J Mol Graph Model 6:203–206
Pyrkov TV, Chugunov AO, Krylov NA, Nolde DE, Efremov RG (2009b) PLATINUM: a web tool for analysis of hydrophobic/hydrophilic organization of biomolecular complexes. Bioinformatics 25:1201–1202
Bohm HJ (1994) The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure. J Comput Aided Mol Des 8:243–256
Eldridge MD, Murray CW, Auton TR, Paolini GV, Mee RP (1997) Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes. J Comput Aided Mol Des 11:425–445
Jones G, Willett P, Glen RC, Leach AR, Taylor R (1997) Development and validation of a genetic algorithm for flexible docking. J Mol Biol 267:727–748
Mooij WTM, Verdonk LM (2005) General and targeted statistical potentials for protein-ligand interactions. Proteins Struct Funct Bioinf 61:272–287
Wang R, Fang X, Lu Y, Wang S (2004) The PDBbind database: collection of binding affinities for protein-ligand complexes with known three-dimensional structures. J Med Chem 47: 2977–2980
Banks JL, Beard HS, Cao Y, Cho AE, Damm W, Farid R, Felts AK, Halgren TA, Mainz DT, Maple JR, Murphy R, Philipp DM, Repasky MP, Zhang LY, Berne BJ, Friesner RA, Gallicchio E, Levy RM (2005) Integrated Modeling Program, Applied Chemical Theory (IMPACT). J Comput Chem 26:1752–1780
Stroganov OV, Novikov FN, Stroylov VS, Kulkov V, Chilov GG (2008) Lead finder: an approach to improve accuracy of protein-ligand docking, binding energy estimation, and virtual screening. J Chem Inf Model 48:2371–2385
Acknowledgments
This work was supported by the Russian Foundation for Basic Research and by the RAS Programmes (MCB and “Basic fundamental research for nanotechnologies and nanomaterials”). Access to computational facilities of the Joint Supercomputer Center RAS (Moscow) and Computer Center of M.V. Lomonosov Moscow State University is gratefully acknowledged.
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Ozerov, I.V., Balitskaya, E.D., Efremov, R.G. (2012). System-Specific Scoring Functions: Application to Guanine-Containing Ligands and Thrombin. In: Puglisi, J., Margaris, M. (eds) Biophysics and Structure to Counter Threats and Challenges. NATO Science for Peace and Security Series B: Physics and Biophysics. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-4923-8_2
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