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Accelerated Molecular Dynamics Simulations of Protein Folding
Author(s) -
Miao Yinglong,
Feixas Ferran,
Eun Changsun,
McCammon J. Andrew
Publication year - 2016
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.24337
Subject(s) - molecular dynamics , folding (dsp implementation) , protein folding , protein dynamics , chemistry , statistical physics , computer science , computational chemistry , physics , biochemistry , electrical engineering , engineering
Folding of four fast‐folding proteins, including chignolin, Trp‐cage, villin headpiece, and WW domain, was simulated via accelerated molecular dynamics (aMD). Free energy profiles calculated through improved reweighting of the aMD simulations using cumulant expansion to the second‐order are in good agreement with those obtained from long‐timescale conventional molecular dynamics simulations. This work demonstrates the enhanced sampling power of aMD on protein folding and will provide basic references in using aMD for further studies.