Assessment of Semiempirical Quantum Mechanical Methods for the Evaluation of Protein Structures.

Journal of Chemical Theory and Computation
Andrew M Wollacott, Kenneth M Merz

Abstract

The ability to discriminate native structures from computer-generated misfolded ones is key to predicting the three-dimensional structure of a protein from its amino acid sequence. Here we describe an assessment of semiempirical methods for discriminating native protein structures from decoy models. The discrimination of decoys entails an analysis of a large number of protein structures, and provides a large-scale validation of quantum mechanical methods and their ability to accurately model proteins. We combine our analysis of semiempirical methods with a comparison of an AMBER force field to discriminate decoys in conjunction with a continuum solvent model. Protein decoys provide a rigorous and reliable benchmark for the evaluation of scoring functions, not only in their ability to accurately identify native structures but also to be computationally tractable to sample a large set of non-native models.

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Jul 1, 2006·Journal of Chemical Theory and Computation·Andrew M Wollacott, Kenneth M Merz

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Citations

Apr 8, 2014·The Journal of Physical Chemistry. B·Berhane TemelsoGeorge C Shields
Apr 8, 2015·Computational and Structural Biotechnology Journal·Nusret Duygu Yilmazer, Martin Korth
May 8, 2014·Journal of Chemical Theory and Computation·Timothy J GieseDarrin M York
Jun 18, 2014·Accounts of Chemical Research·Timothy J GieseDarrin M York
Aug 30, 2008·Journal of Computational Chemistry·Victor M Anisimov, Vladislav L Bugaenko
Nov 1, 2011·Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry·Martin Korth
Jul 3, 2013·Journal of Chemical Theory and Computation·Timothy J GieseDarrin M York
Jul 1, 2020·Journal of Computer-aided Molecular Design·Natalie M ColodetteEliezer J Barreiro
Mar 27, 2009·The Journal of Physical Chemistry. B·Xiao HeKenneth M Merz
Jan 12, 2010·Journal of Chemical Theory and Computation·Martin KorthPavel Hobza
Sep 11, 2012·Journal of Chemical Theory and Computation·Julio Daniel Carvalho MaiaGerd B Rocha

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