Folding in lattice models with side chains

DOI10.1016/S0010-4655(02)00349-1MaRDI QIDQ696683zbMATH OpenFDO

Authors Mai Suan Li, D. K. Klimov, D. Thirumalai

Publication date 12 September 2002

Published in Computer Physics Communications (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/cond-mat/0211348

zbMATH Keywords

Monte CarloLattice modelProtein foldingSide chain

Mathematics Subject Classification ID

Dynamic lattice systems (kinetic Ising, etc.) and systems on graphs in time-dependent statistical mechanics (82C20)

Abstract: The folding kinetics of three-dimensional lattice Go models with side chains is studied using two different Monte Carlo move sets. A flexible move set based on single, double and triple backbone moves is found to be far superior compared to the standard Monte Carlo dynamics. It was found that the folding time grows as a power law with the chain length and the corresponding exponent $lambdaapprox3.6$ for Go models. The study shows that the incorporation of side chains dramatically slows down folding rates.

Cited in

(1)

• An integer programming model for protein structure prediction using the 3D-HP side chain model

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