The ruggedness of protein–protein energy landscape and the cutoff for 1/r n potentials | Zendy

Anatoly M. Ruvinsky | Zendy; Ilya A. Vakser | Zendy

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The ruggedness of protein–protein energy landscape and the cutoff for 1/r n potentials

Author(s) -

Anatoly M. Ruvinsky,

Ilya A. Vakser

Publication year - 2009

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btp108

Subject(s) - cutoff , energy landscape , energy (signal processing) , physics , statistical physics , biology , biochemistry , quantum mechanics

Computational studies of the energetics of protein association are important for revealing the underlying fundamental principles and for designing better tools to model protein complexes. The interaction cutoff contribution to the ruggedness of protein-protein energy landscape is studied in terms of relative energy fluctuations for 1/r(n) potentials based on a simplistic model of a protein complex. This artificial ruggedness exists for short cutoffs and gradually disappears with the cutoff increase.

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