System-Specific Scoring Functions: Application to Guanine-Containing Ligands and Thrombin
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.
KeywordsMolecular Docking Scoring Function Weighting Coefficient Rotatable Bond Conformational Search
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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