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Energy minimizations with a combination of two knowledge‐based potentials for protein folding
Author(s) -
de Sancho David,
Rey Antonio
Publication year - 2008
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.20924
Subject(s) - force field (fiction) , folding (dsp implementation) , computer science , energy minimization , protein folding , simple (philosophy) , work (physics) , set (abstract data type) , minification , energy (signal processing) , molecular dynamics , hydrogen bond , potential energy , process (computing) , algorithm , biological system , computational chemistry , chemistry , molecule , artificial intelligence , physics , thermodynamics , classical mechanics , engineering , mechanical engineering , biochemistry , philosophy , epistemology , quantum mechanics , biology , programming language , organic chemistry , operating system
New force fields that are both simple and accurate are needed for computationally efficient molecular simulation studies to give insight into the actual features of the protein folding process. In this work, we assess a force field based on a new combination of two coarse‐grained potentials taken from the bibliography. These potentials have already been proved efficient in representing different types of interactions, namely the side‐chain interactions and the backbone hydrogen bonds. Now we combine them weighing their contribution to the global energy with a very simplified parameterization. To assess this combination of potentials, we use our evolutionary method to carry out energy minimization experiments for a set of all‐α, all‐β, and (α + β) protein structures. Our results, based on the assembly of short rigid native fragments, suggest that this combination of potentials can be successfully employed in coarse‐grained folding simulations. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008