Temperature–pressure shuffling outlier flooding method enhances the conformational sampling of proteins |
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| Authors: | Ryuhei Harada Ryunosuke Yoshino Hiroaki Nishizawa Yasuteru Shigeta |
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| Institution: | 1. Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan;2. Transborder Medical Research Center, University of Tsukuba, 1-1-1 Tenodai Tsukuba, Ibaraki 305-8577, Japan |
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| Abstract: | Outlier flooding method (OFLOOD) is an efficient conformational sampling method developed by the authors. In the present study, to further enhance the conformational sampling efficiency, a set of parameters (temperatures and pressures) specified as inputs in the original OFLOOD were shuffled before restarting the short-time molecular dynamics (MD) simulations. Because of the diversity of these parameters, it was confirmed that the extended OFLOOD becomes superior to the original one in finding the folding pathways of Trp-cage. © 2019 Wiley Periodicals, Inc. |
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| Keywords: | Molecular Dynamics Protein Folding Enhanced Sampling of Proteins Extended OFLOOD Trp-Cage |
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