Protein-protein docking refinement using restraint molecular dynamics simulations

• Autorzy: Zacharias M.

Identyfikatory

DOI

10.17466/tq2016/20.4/d

• Języki publikacji: EN

Abstrakty

EN

A realistic prediction of the structure of protein-protein complexes is of major importance to obtain three-dimensional models for the interaction of proteins to form complexes and assemblies. In addition to the systematic search for putative binding sites on the surface of two binding partners, the second step of a docking effort, the refinement of docked complexes, is a major bottleneck to obtain realistic interaction geometries. Typically, the first initial systematic search employs rigid partner structures or few flexible degrees of freedom, whereas the refinement step involves fully flexible partner structures. The possibility to refine docked complexes using restraint MD simulations combined with an implicit solvent (Generalized Born) mode l was explored on three example test complexes starting from unbound partner structures. Significant improvement, both in scoring and agreement with the native complex structure after refinement was observed for two test cases. No improvement was found for a test case of a complex with lower binding affinity. The method can be easily applied to any docked protein-protein complex, however, more general applicability requires further improvements in the scoring function.

Słowa kluczowe

EN

protein-protein complex; docking prediction; force field modeling; implicit solvent modeling

• Wydawca: Politechnika Gdańska
• Czasopismo: TASK Quarterly : scientific bulletin of Academic Computer Centre in Gdansk
• Rocznik: 2016
• Tom: Vol. 20, No 4
• Strony: 353--360
• Opis fizyczny: Bibliogr. 11 poz., rys.

Twórcy

autor

Zacharias M.

• Physics Department T38, Technical University of Munich, James-Franck-Str. 1, 85748 Garching, Germany

Bibliografia

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