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Temperature-dependent probabilistic roadmap algorithm for calculating variationally optimized conformational transition pathways

delete2006-11-15
delete24
PRE
AI
H
Haijun Yang
H
Hao Wu
D
Dawei Li
L
Li Han *
S
Shuanghong Huo
DOI：10.1021/ct0502054delete
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Abstract

Abstract

En 中文
In this paper we present a method to calculate a temperature-dependent optimized conformational transition pathways. This method is based on the maximization of the flux derived from the Smoluchowski equation and is implemented with a probabilistic roadmap algorithm. We have tested the algorithm on four systemsthe MUller potential, the three-hole potential, alanine dipeptide, and the folding of beta-hairpin. Comparison is made with existing algorithms designed for the calculation of protein conformational transition and folding pathways. The applications demonstrate the ability of the algorithm to isolate a temperature-dependent optimal reaction path with improved sampling and efficiency.
Keywords:
BETA-HAIRPIN FORMATION
MOLECULAR-DYNAMICS SIMULATIONS
NUDGED ELASTIC BAND
PROTEIN-FOLDING PATHWAYS
FREE-ENERGY LANDSCAPE
C-TERMINAL FRAGMENT
ALL-ATOM MODEL
REACTION PATHS
REACTION COORDINATE
CLASSICAL TRAJECTORIES
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Journal

Journal of Chemical Theory and Computation cover
Journal of Chemical Theory and Computation
IF:
5.5
Papers:
1.1W
Citations:
5.4W

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