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• W3037337145 abstract "Traditional molecular dynamics (MD) simulations have difficulties in tracking the slow molecular motions, at least partially due to the waste of sampling in already sampled regions. Here, we proposed a new enhanced sampling method, expansion sampling (FEXS), to improve the sampling efficiency of molecular simulations by iteratively selecting seed structures diversely distributed at the frontier of an already sampled region to initiate new simulations. Different from other enhanced sampling methods, FEXS identifies the frontier seeds by integrating the Gaussian mixture model and the convex hull algorithm, which effectively improves the structural variation among the selected seeds and thus the descendant simulations. Validation in three protein systems, including the folding of chignolin, open-to-closed transition of maltodextrin binding protein, and internal conformational change of bovine pancreatic trypsin inhibitor, confirmed the effectiveness of this novel method in enhancing the sampling of conventional MD simulations to observe the large-scale protein conformational changes. When compared with other enhanced sampling methods like the structural dissimilarity sampling (SDS), FEXS reached at least the same level of sampling efficiency but was capable of providing complementary information in the three tested protein systems." @default.
• W3037337145 created "2020-07-02" @default.
• W3037337145 creator A5079023600 @default.
• W3037337145 creator A5080207299 @default.
• W3037337145 date "2020-06-25" @default.
• W3037337145 modified "2023-09-29" @default.
• W3037337145 title "Frontier Expansion Sampling: A Method to Accelerate Conformational Search by Identifying Novel Seed Structures for Restart" @default.
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• W3037337145 doi "https://doi.org/10.1021/acs.jctc.0c00064" @default.
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• W3037337145 hasPublicationYear "2020" @default.
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