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Development and Benchmarking of Open Force Field v1.0.0-the Parsley Small-Molecule Force Field.
Qiu, Yudong; Smith, Daniel G A; Boothroyd, Simon; Jang, Hyesu; Hahn, David F; Wagner, Jeffrey; Bannan, Caitlin C; Gokey, Trevor; Lim, Victoria T; Stern, Chaya D; Rizzi, Andrea; Tjanaka, Bryon; Tresadern, Gary; Lucas, Xavier; Shirts, Michael R; Gilson, Michael K; Chodera, John D; Bayly, Christopher I; Mobley, David L; Wang, Lee-Ping.
Afiliación
  • Qiu Y; Chemistry Department, The University of California at Davis, Davis, California 95616, United States.
  • Smith DGA; The Molecular Sciences Software Institute (MolSSI), Blacksburg, Virginia 24060, United States.
  • Boothroyd S; Computational & Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States.
  • Jang H; Chemistry Department, The University of California at Davis, Davis, California 95616, United States.
  • Hahn DF; Computational Chemistry, Janssen Research & Development, Turnhoutseweg 30, Beerse B-2340, Belgium.
  • Wagner J; Chemistry Department, The University of California at Irvine, Irvine, California 92617, United States.
  • Bannan CC; Chemistry Department, The University of California at Irvine, Irvine, California 92617, United States.
  • Gokey T; Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California at San Diego, La Jolla, California 92093, United States.
  • Lim VT; Chemistry Department, The University of California at Irvine, Irvine, California 92617, United States.
  • Stern CD; Chemistry Department, The University of California at Irvine, Irvine, California 92617, United States.
  • Rizzi A; Computational & Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States.
  • Tjanaka B; Computational & Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States.
  • Tresadern G; Tri-Institutional Training Program in Computational Biology and Medicine, New York, New York 10065, United States.
  • Lucas X; Chemistry Department, The University of California at Irvine, Irvine, California 92617, United States.
  • Shirts MR; Computational Chemistry, Janssen Research & Development, Turnhoutseweg 30, Beerse B-2340, Belgium.
  • Gilson MK; F. Hoffmann-La Roche AG, Basel 4070, Switzerland.
  • Chodera JD; Chemical & Biological Engineering Department, The University of Colorado at Boulder, Boulder, Colorado 80309, United States.
  • Bayly CI; Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California at San Diego, La Jolla, California 92093, United States.
  • Mobley DL; Computational & Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States.
  • Wang LP; OpenEye Scientific Software, Santa Fe, New Mexico 87508, United States.
J Chem Theory Comput ; 17(10): 6262-6280, 2021 Oct 12.
Article en En | MEDLINE | ID: mdl-34551262
We present a methodology for defining and optimizing a general force field for classical molecular simulations, and we describe its use to derive the Open Force Field 1.0.0 small-molecule force field, codenamed Parsley. Rather than using traditional atom typing, our approach is built on the SMIRKS-native Open Force Field (SMIRNOFF) parameter assignment formalism, which handles increases in the diversity and specificity of the force field definition without needlessly increasing the complexity of the specification. Parameters are optimized with the ForceBalance tool, based on reference quantum chemical data that include torsion potential energy profiles, optimized gas-phase structures, and vibrational frequencies. These quantum reference data are computed and are maintained with QCArchive, an open-source and freely available distributed computing and database software ecosystem. In this initial application of the method, we present essentially a full optimization of all valence parameters and report tests of the resulting force field against compounds and data types outside the training set. These tests show improvements in optimized geometries and conformational energetics and demonstrate that Parsley's accuracy for liquid properties is similar to that of other general force fields, as is accuracy on binding free energies. We find that this initial Parsley force field affords accuracy similar to that of other general force fields when used to calculate relative binding free energies spanning 199 protein-ligand systems. Additionally, the resulting infrastructure allows us to rapidly optimize an entirely new force field with minimal human intervention.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Benchmarking / Petroselinum Límite: Humans Idioma: En Revista: J Chem Theory Comput Año: 2021 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Estados Unidos
Texto completo
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Imprimir
XML
PubMed Links
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Benchmarking / Petroselinum Límite: Humans Idioma: En Revista: J Chem Theory Comput Año: 2021 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Estados Unidos