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Optimization of protein models
Author(s) -
Gront Dominik,
Kmiecik Sebastian,
Blaszczyk Maciej,
Ekonomiuk Dariusz,
Koliński Andrzej
Publication year - 2012
Publication title -
wiley interdisciplinary reviews: computational molecular science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 5.126
H-Index - 81
eISSN - 1759-0884
pISSN - 1759-0876
DOI - 10.1002/wcms.1090
Subject(s) - monte carlo method , variety (cybernetics) , protein structure prediction , computer science , molecular dynamics , statistical physics , statistical mechanics , protein structure , chemistry , mathematics , physics , computational chemistry , artificial intelligence , statistics , biochemistry
Abstract Protein structure predictions, and experimentally derived protein structures, very often require certain structure improvement (refinement), which means bringing it closer to real, usually in vivo working conformations. In respect to the variety of protein models to be refined, computational optimization procedures could be divided into localized (applied to a small part of a structure) and global (whole structure). Generally speaking, the first problem is usually tractable, and the latter remains to be extremely challenging for systems larger then peptides or small proteins: optimization complexity and difficulty dramatically increase with the size of structures to be optimized. © 2012 John Wiley & Sons, Ltd. This article is categorized under: Molecular and Statistical Mechanics > Molecular Dynamics and Monte-Carlo Methods