Protein–ligand docking using FFT based sampling: D3R case study |
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| Authors: | Dzmitry Padhorny David R Hall Hanieh Mirzaei Artem B Mamonov Mohammad Moghadasi Andrey Alekseenko Dmitri Beglov Dima Kozakov |
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| Institution: | 1.Department of Applied Mathematics and Statistics,Stony Brook University,Stony Brook,USA;2.Laufer Center for Physical and Quantitative Biology,Stony Brook University,Stony Brook,USA;3.Acpharis Inc.,Holliston,USA;4.Department of Biomedical Engineering,Boston University,Boston,USA;5.Moscow Institute of Physics and Technology (State University),Dolgoprudny, Moscow Oblast,Russia;6.Institute of Computer Aided Design of the Russian Academy of Sciences,Moscow,Russia |
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| Abstract: | Fast Fourier transform (FFT) based approaches have been successful in application to modeling of relatively rigid protein–protein complexes. Recently, we have been able to adapt the FFT methodology to treatment of flexible protein–peptide interactions. Here, we report our latest attempt to expand the capabilities of the FFT approach to treatment of flexible protein–ligand interactions in application to the D3R PL-2016-1 challenge. Based on the D3R assessment, our FFT approach in conjunction with Monte Carlo minimization off-grid refinement was among the top performing methods in the challenge. The potential advantage of our method is its ability to globally sample the protein–ligand interaction landscape, which will be explored in further applications. |
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