Focused grid‐based resampling for protein docking and mapping |
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| Authors: | Artem B Mamonov Mohammad Moghadasi Hanieh Mirzaei Shahrooz Zarbafian Laurie E Grove Tanggis Bohnuud Pirooz Vakili Ioannis Ch Paschalidis Sandor Vajda Dima Kozakov |
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| Institution: | 1. Department of Biomedical Engineering, Boston University, Boston, Massachusetts;2. Center for Information and Systems Engineering, Boston University, Boston, Massachusetts;3. Department of Mechanical Engineering, Boston University, Boston, Massachusetts;4. Department of Sciences, Wentworth Institute of Technology, Boston, Massachusetts;5. Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts;6. Department of Chemistry, Boston University, Boston, Massachusetts;7. Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York |
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| Abstract: | 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. |
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| Keywords: | protein‐protein docking protein mapping fast Fourier transform systematic sampling binding hot spots |
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