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Comparison of Stochastic Optimization Methods for All‐Atom Folding of the Trp‐Cage Protein
Author(s) -
Schug Alexander,
Herges Thomas,
Verma Abhinav,
Lee Kyu Hwan,
Wenzel Wolfgang
Publication year - 2005
Publication title -
chemphyschem
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.016
H-Index - 140
eISSN - 1439-7641
pISSN - 1439-4235
DOI - 10.1002/cphc.200500213
Subject(s) - parallel tempering , protein data bank (rcsb pdb) , atom (system on chip) , folding (dsp implementation) , protein folding , force field (fiction) , cage , chemistry , potential energy surface , biological system , chemical physics , computational chemistry , crystallography , computer science , molecule , stereochemistry , mathematics , biochemistry , biology , artificial intelligence , combinatorics , engineering , embedded system , bayesian probability , organic chemistry , markov chain monte carlo , monte carlo molecular modeling , electrical engineering
The performances of three different stochastic optimization methods for all‐atom protein structure prediction are investigated and compared. We use the recently developed all‐atom free‐energy force field (PFF01), which was demonstrated to correctly predict the native conformation of several proteins as the global optimum of the free energy surface. The trp‐cage protein (PDB‐code 1L2Y) is folded with the stochastic tunneling method, a modified parallel tempering method, and the basin‐hopping technique. All the methods correctly identify the native conformation, and their relative efficiency is discussed.