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Zhang, Dawei; Lazim, Raudah; Mun Yip, Yew, E-mail: sunstar53@126.com, E-mail: siti13@e.ntu.edu.sg2017
AbstractAbstract
[en] Highlights: • Polarizable force field PHB was applied to fold a hybrid protein FSD-EY. • The effect of reducing the polarization effect integrated into the force field by the PHB model was also examined. • Precise folding of the β-sheet of FSD-EY was further achieved by relaxing the REMD structure in explicit water. We conducted an all-atom ab initio folding of FSD-EY, a protein with a ββα configuration using non-polarizable (AMBER) and polarizable force fields (PHB designed by Gao et al.) in implicit solvent. The effect of reducing the polarization effect integrated into the force field by the PHB model, termed the PHB0.7 was also examined in the folding of FSD-EY. This model incorporates into the force field 70% of the original polarization effect to minimize the likelihood of over-stabilizing the backbone hydrogen bonds. Precise folding of the β-sheet of FSD-EY was further achieved by relaxing the REMD structure obtained in explicit water.
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S0009261417305596; Available from http://dx.doi.org/10.1016/j.cplett.2017.06.020; Copyright (c) 2017 Elsevier B.V. All rights reserved.; Country of input: International Atomic Energy Agency (IAEA)
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Journal Article
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