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Ab initio protein structure prediction with force field parameters derived from water‐phase quantum chemical calculation
Author(s) -
Katagiri Daisuke,
Fuji Hideyoshi,
Neya Saburo,
Hoshino Tyuji
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.20963
Subject(s) - force field (fiction) , ab initio , molecular dynamics , protein structure prediction , computational chemistry , chemistry , stability (learning theory) , field (mathematics) , protein structure , ab initio quantum chemistry methods , statistical physics , physics , molecule , quantum mechanics , computer science , mathematics , biochemistry , machine learning , pure mathematics , organic chemistry
Molecular dynamics (MD) simulations are extensively used in the study of the structures and functions of proteins. Ab initio protein structure prediction is one of the most important subjects in computational biology, and many trials have been performed using MD simulation so far. Since the results of MD simulations largely depend on the force field, reliable force field parameters are indispensable for the success of MD simulation. In this work, we have modified atom charges in a standard force field on the basis of water‐phase quantum chemical calculations. The modified force field turned out appropriate for ab initio protein structure prediction by the MD simulation with the generalized Born method. Detailed analysis was performed in terms of the conformational stability of amino acid residues, the stability of secondary structure of proteins, and the accuracy for prediction of protein tertiary structure, comparing the modified force field with a standard one. The energy balance between α‐helix and β‐sheet structures was significantly improved by the modification of charge parameters. © 2008 Wiley Periodicals, Inc. J Comput Chem 2008