System-Specific Scoring Functions: Application to Guanine-Containing Ligands and Thrombin

  • Ivan V. Ozerov
  • Elisabeth D. Balitskaya
  • Roman G. Efremov
Conference paper
First Online:
Part of the NATO Science for Peace and Security Series B: Physics and Biophysics book series (NAPSB)

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.

Keywords

Molecular Docking Scoring Function Weighting Coefficient Rotatable Bond Conformational Search 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
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Notes

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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Copyright information

© Springer Science+Business Media Dordrecht 2012

Authors and Affiliations

  • Ivan V. Ozerov
    • 1
    • 2
  • Elisabeth D. Balitskaya
    • 1
    • 2
  • Roman G. Efremov
    • 1
  1. 1.Laboratory of Biomolecular ModelingRussian Academy of Sciences, M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic ChemistryMoscowRussia
  2. 2.Department of BioengineeringM.V. Lomonosov Moscow State University, Biological facultyMoscowRussia

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