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Improved Peptide and Protein Torsional Energetics with the OPLS-AA Force Field

[Image: see text] The development and validation of new peptide dihedral parameters are reported for the OPLS-AA force field. High accuracy quantum chemical methods were used to scan φ, ψ, χ(1), and χ(2) potential energy surfaces for blocked dipeptides. New Fourier coefficients for the dihedral angl...

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Autores principales: Robertson, Michael J., Tirado-Rives, Julian, Jorgensen, William L.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Chemical Society 2015
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4504185/
https://www.ncbi.nlm.nih.gov/pubmed/26190950
http://dx.doi.org/10.1021/acs.jctc.5b00356
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author Robertson, Michael J.
Tirado-Rives, Julian
Jorgensen, William L.
author_facet Robertson, Michael J.
Tirado-Rives, Julian
Jorgensen, William L.
author_sort Robertson, Michael J.
collection PubMed
description [Image: see text] The development and validation of new peptide dihedral parameters are reported for the OPLS-AA force field. High accuracy quantum chemical methods were used to scan φ, ψ, χ(1), and χ(2) potential energy surfaces for blocked dipeptides. New Fourier coefficients for the dihedral angle terms of the OPLS-AA force field were fit to these surfaces, utilizing a Boltzmann-weighted error function and systematically examining the effects of weighting temperature. To prevent overfitting to the available data, a minimal number of new residue-specific and peptide-specific torsion terms were developed. Extensive experimental solution-phase and quantum chemical gas-phase benchmarks were used to assess the quality of the new parameters, named OPLS-AA/M, demonstrating significant improvement over previous OPLS-AA force fields. A Boltzmann weighting temperature of 2000 K was determined to be optimal for fitting the new Fourier coefficients for dihedral angle parameters. Conclusions are drawn from the results for best practices for developing new torsion parameters for protein force fields.
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spelling pubmed-45041852015-07-17 Improved Peptide and Protein Torsional Energetics with the OPLS-AA Force Field Robertson, Michael J. Tirado-Rives, Julian Jorgensen, William L. J Chem Theory Comput [Image: see text] The development and validation of new peptide dihedral parameters are reported for the OPLS-AA force field. High accuracy quantum chemical methods were used to scan φ, ψ, χ(1), and χ(2) potential energy surfaces for blocked dipeptides. New Fourier coefficients for the dihedral angle terms of the OPLS-AA force field were fit to these surfaces, utilizing a Boltzmann-weighted error function and systematically examining the effects of weighting temperature. To prevent overfitting to the available data, a minimal number of new residue-specific and peptide-specific torsion terms were developed. Extensive experimental solution-phase and quantum chemical gas-phase benchmarks were used to assess the quality of the new parameters, named OPLS-AA/M, demonstrating significant improvement over previous OPLS-AA force fields. A Boltzmann weighting temperature of 2000 K was determined to be optimal for fitting the new Fourier coefficients for dihedral angle parameters. Conclusions are drawn from the results for best practices for developing new torsion parameters for protein force fields. American Chemical Society 2015-06-01 2015-07-14 /pmc/articles/PMC4504185/ /pubmed/26190950 http://dx.doi.org/10.1021/acs.jctc.5b00356 Text en Copyright © 2015 American Chemical Society This is an open access article published under an ACS AuthorChoice License (http://pubs.acs.org/page/policy/authorchoice_termsofuse.html) , which permits copying and redistribution of the article or any adaptations for non-commercial purposes.
spellingShingle Robertson, Michael J.
Tirado-Rives, Julian
Jorgensen, William L.
Improved Peptide and Protein Torsional Energetics with the OPLS-AA Force Field
title Improved Peptide and Protein Torsional Energetics with the OPLS-AA Force Field
title_full Improved Peptide and Protein Torsional Energetics with the OPLS-AA Force Field
title_fullStr Improved Peptide and Protein Torsional Energetics with the OPLS-AA Force Field
title_full_unstemmed Improved Peptide and Protein Torsional Energetics with the OPLS-AA Force Field
title_short Improved Peptide and Protein Torsional Energetics with the OPLS-AA Force Field
title_sort improved peptide and protein torsional energetics with the opls-aa force field
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4504185/
https://www.ncbi.nlm.nih.gov/pubmed/26190950
http://dx.doi.org/10.1021/acs.jctc.5b00356
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