Multiplexed-Replica Exchange Molecular Dynamics Method for Protein Folding Simulation
نویسندگان
چکیده
منابع مشابه
Multiplexed-replica exchange molecular dynamics method for protein folding simulation.
Simulating protein folding thermodynamics starting purely from a protein sequence is a grand challenge of computational biology. Here, we present an algorithm to calculate a canonical distribution from molecular dynamics simulation of protein folding. This algorithm is based on the replica exchange method where the kinetic trapping problem is overcome by exchanging noninteracting replicas simul...
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We show how accurate kinetic information, such as the rates of protein folding and unfolding, can be extracted from replica-exchange molecular dynamics (REMD) simulations. From the brief and continuous trajectory segments between replica exchanges, we estimate short-time propagators in conformation space and use them to construct a master equation. For a helical peptide in explicit water, we de...
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The replica exchange molecular dynamics ~REMD! approach is applied to a 20-residue three-stranded antiparallel b-sheet peptide. At physiologically relevant temperature REMD samples conformational space much more efficiently than constant temperature molecular dynamics ~MD! and allows reversible folding ~312 folding events during a total simulation time of 32 ms!. The energetic and structural pr...
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The folding process of the 20 residue Trp-cage mini-protein was investigated using standard temperature replica exchange molecular dynamics (T-RexMD) simulation and a biasing potential RexMD (BP-RexMD) method. In contrast to several conventional molecular dynamics simulations, both RexMD methods sampled conformations close to the native structure after 10-20 ns simulation time as the dominant c...
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We sketch the statistical physics framework of the replica exchange technique when applied to molecular dynamics simulations. In particular, we draw attention to generalized move sets that allow a variety of optimizations as well as new applications of the method.
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ژورنال
عنوان ژورنال: Biophysical Journal
سال: 2003
ISSN: 0006-3495
DOI: 10.1016/s0006-3495(03)74897-8