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A quantum chemical method for rapid optimization of protein structures
Author(s) -
Wada Mitsuhito,
Sakurai Minoru
Publication year - 2004
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.20154
Subject(s) - quantum chemical , broyden–fletcher–goldfarb–shanno algorithm , computer science , scaling , linear scale , energy minimization , quantum , optimization algorithm , algorithm , mathematical optimization , chemistry , mathematics , computational chemistry , geometry , molecule , physics , quantum mechanics , computer network , asynchronous communication , organic chemistry , geodesy , geography
A quantum chemical method for rapid optimization of protein structures is proposed. In this method, a protein structure is treated as an assembly of amino acid units, and the geometry optimization of each unit is performed with taking the effect of its surrounding environment into account. The optimized geometry of a whole protein is obtained by repeated application of such a local optimization procedure over the entire part of the protein. Here, we implemented this method in the MOPAC program and performed geometry optimization for three different sizes of proteins. Consequently, these results demonstrate that the total energies of the proteins are much efficiently minimized compared with the use of conventional optimization methods, including the MOZYME algorithm (a representative linear‐scaling method) with the BFGS routine. The proposed method is superior to the conventional methods in both CPU time and memory requirements. © 2004 Wiley Periodicals, Inc. J Comput Chem 26: 160–168, 2005