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Multicanonical parallel simulations of proteins with continuous potentials
Author(s) -
Hayryan Shura,
Hu ChinKun,
Hu ShunYun,
Shang RungJi
Publication year - 2001
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.1086
Subject(s) - simulated annealing , computation , monte carlo method , sequence (biology) , amino acid residue , computer science , protein structure prediction , molecular dynamics , statistical physics , simple (philosophy) , amino acid , algorithm , peptide sequence , protein structure , chemistry , computational chemistry , physics , mathematics , biochemistry , statistics , philosophy , epistemology , gene
The determination of the three‐dimensional (3D) structure of a protein or peptide is a very important research problem in biological and medical sciences. Anfinsen's experiments (Science 1973, 181, 223) on renaturation of denatured proteins have shown that the native 3D structure of a (small) protein at low (room) temperatures is uniquely determined by its amino acid sequence, which suggests that it might be possible to determine the 3D structure of a protein from its amino acid sequence by pure computations. As a step toward that goal, in this article we present a simple approach for parallelization of multicanonical Monte Carlo simulations of proteins with continuous potentials. Our method is based on the parallel calculation of the protein energy function. The algorithm is tested by simulated annealing and multicanonical simulations of two small peptides, and known results are reproduced accurately. An acceptable degree of parallelization can be achieved in the simulation of Protein L using up to 30 PCs. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1287–1296, 2001