| Kalina Atkovska, Sergey Samsonov and Maria Teresa Pisabarro all from the Structural Bioinformatics Group, BIOTEC, TU Dresden. Molecular docking is a method of predicting the conformation of a ligand in a targeted binding site, and it provides the information about the putative structure and binding affinity of the complex. Molecular docking has proven to be particularly useful for the study of interactions of proteins with different classes of molecules: small ligands (drugs), sugars, peptides and proteins; however it is severely limited by the imperfections in the applied scoring schemes. Several studies of the most commonly used docking software have shown a poor correlation between the docking scores and the experimentally observed binding affinities, even if they were to some extent capable of predicting the correct pose (1,2). One reason for this observation might be the fact that most computational methods take only one unique top scoring binding pose into account, while in nature there might be several binding poses with comparable energies, which contribute to the binding energy of the complex. This work represents a high-throughput docking study aiming to explore if a better agreement between computational and experimental data can be obtained by taking into account multipose binding. 1.Plewczynski, D., Łaźniewski, M., Augustyniak, R. and Ginalski, K. (2010) Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database. Journal of Computational Chemistry 32(4), 742-755 2. Smith, R.D., Dunbar, J.B., Ung, P.M., Esposito, E.X., Yang, C., Wang, S. and Carlson, H.A. (2011) CSAR Benchmark Exercise of 2010: Combined Evaluation Across All Submitted Scoring Functions. Journal of Chemical Information and Modeling 51(9), 2115-2131 |
|