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Focused grid‐based resampling for protein docking and mapping
Author(s) -
Mamonov Artem B.,
Moghadasi Mohammad,
Mirzaei Hanieh,
Zarbafian Shahrooz,
Grove Laurie E.,
Bohnuud Tanggis,
Vakili Pirooz,
Ch. Paschalidis Ioannis,
Vajda Sandor,
Kozakov Dima
Publication year - 2016
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.24273
Subject(s) - docking (animal) , fast fourier transform , resampling , cluster (spacecraft) , grid , computer science , chemistry , algorithm , biological system , mathematics , biology , geometry , medicine , nursing , programming language
The fast Fourier transform (FFT) sampling algorithm has been used with success in application to protein‐protein docking and for protein mapping, the latter docking a variety of small organic molecules for the identification of binding hot spots on the target protein. Here we explore the local rather than global usage of the FFT sampling approach in docking applications. If the global FFT based search yields a near‐native cluster of docked structures for a protein complex, then focused resampling of the cluster generally leads to a substantial increase in the number of conformations close to the native structure. In protein mapping, focused resampling of the selected hot spot regions generally reveals further hot spots that, while not as strong as the primary hot spots, also contribute to ligand binding. The detection of additional ligand binding regions is shown by the improved overlap between hot spots and bound ligands. © 2016 Wiley Periodicals, Inc.