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Development and Benchmarking of Open Force Field 2.0.0: The Sage Small Molecule Force Field

[Image: see text] We introduce the Open Force Field (OpenFF) 2.0.0 small molecule force field for drug-like molecules, code-named Sage, which builds upon our previous iteration, Parsley. OpenFF force fields are based on direct chemical perception, which generalizes easily to highly diverse sets of c...

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Detalles Bibliográficos
Autores principales: Boothroyd, Simon, Behara, Pavan Kumar, Madin, Owen C., Hahn, David F., Jang, Hyesu, Gapsys, Vytautas, Wagner, Jeffrey R., Horton, Joshua T., Dotson, David L., Thompson, Matthew W., Maat, Jessica, Gokey, Trevor, Wang, Lee-Ping, Cole, Daniel J., Gilson, Michael K., Chodera, John D., Bayly, Christopher I., Shirts, Michael R., Mobley, David L.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Chemical Society 2023
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10269353/
https://www.ncbi.nlm.nih.gov/pubmed/37167319
http://dx.doi.org/10.1021/acs.jctc.3c00039
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author Boothroyd, Simon
Behara, Pavan Kumar
Madin, Owen C.
Hahn, David F.
Jang, Hyesu
Gapsys, Vytautas
Wagner, Jeffrey R.
Horton, Joshua T.
Dotson, David L.
Thompson, Matthew W.
Maat, Jessica
Gokey, Trevor
Wang, Lee-Ping
Cole, Daniel J.
Gilson, Michael K.
Chodera, John D.
Bayly, Christopher I.
Shirts, Michael R.
Mobley, David L.
author_facet Boothroyd, Simon
Behara, Pavan Kumar
Madin, Owen C.
Hahn, David F.
Jang, Hyesu
Gapsys, Vytautas
Wagner, Jeffrey R.
Horton, Joshua T.
Dotson, David L.
Thompson, Matthew W.
Maat, Jessica
Gokey, Trevor
Wang, Lee-Ping
Cole, Daniel J.
Gilson, Michael K.
Chodera, John D.
Bayly, Christopher I.
Shirts, Michael R.
Mobley, David L.
author_sort Boothroyd, Simon
collection PubMed
description [Image: see text] We introduce the Open Force Field (OpenFF) 2.0.0 small molecule force field for drug-like molecules, code-named Sage, which builds upon our previous iteration, Parsley. OpenFF force fields are based on direct chemical perception, which generalizes easily to highly diverse sets of chemistries based on substructure queries. Like the previous OpenFF iterations, the Sage generation of OpenFF force fields was validated in protein–ligand simulations to be compatible with AMBER biopolymer force fields. In this work, we detail the methodology used to develop this force field, as well as the innovations and improvements introduced since the release of Parsley 1.0.0. One particularly significant feature of Sage is a set of improved Lennard-Jones (LJ) parameters retrained against condensed phase mixture data, the first refit of LJ parameters in the OpenFF small molecule force field line. Sage also includes valence parameters refit to a larger database of quantum chemical calculations than previous versions, as well as improvements in how this fitting is performed. Force field benchmarks show improvements in general metrics of performance against quantum chemistry reference data such as root-mean-square deviations (RMSD) of optimized conformer geometries, torsion fingerprint deviations (TFD), and improved relative conformer energetics (ΔΔE). We present a variety of benchmarks for these metrics against our previous force fields as well as in some cases other small molecule force fields. Sage also demonstrates improved performance in estimating physical properties, including comparison against experimental data from various thermodynamic databases for small molecule properties such as ΔH(mix), ρ(x), ΔG(solv), and ΔG(trans). Additionally, we benchmarked against protein–ligand binding free energies (ΔG(bind)), where Sage yields results statistically similar to previous force fields. All the data is made publicly available along with complete details on how to reproduce the training results at https://github.com/openforcefield/openff-sage.
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spelling pubmed-102693532023-06-16 Development and Benchmarking of Open Force Field 2.0.0: The Sage Small Molecule Force Field Boothroyd, Simon Behara, Pavan Kumar Madin, Owen C. Hahn, David F. Jang, Hyesu Gapsys, Vytautas Wagner, Jeffrey R. Horton, Joshua T. Dotson, David L. Thompson, Matthew W. Maat, Jessica Gokey, Trevor Wang, Lee-Ping Cole, Daniel J. Gilson, Michael K. Chodera, John D. Bayly, Christopher I. Shirts, Michael R. Mobley, David L. J Chem Theory Comput [Image: see text] We introduce the Open Force Field (OpenFF) 2.0.0 small molecule force field for drug-like molecules, code-named Sage, which builds upon our previous iteration, Parsley. OpenFF force fields are based on direct chemical perception, which generalizes easily to highly diverse sets of chemistries based on substructure queries. Like the previous OpenFF iterations, the Sage generation of OpenFF force fields was validated in protein–ligand simulations to be compatible with AMBER biopolymer force fields. In this work, we detail the methodology used to develop this force field, as well as the innovations and improvements introduced since the release of Parsley 1.0.0. One particularly significant feature of Sage is a set of improved Lennard-Jones (LJ) parameters retrained against condensed phase mixture data, the first refit of LJ parameters in the OpenFF small molecule force field line. Sage also includes valence parameters refit to a larger database of quantum chemical calculations than previous versions, as well as improvements in how this fitting is performed. Force field benchmarks show improvements in general metrics of performance against quantum chemistry reference data such as root-mean-square deviations (RMSD) of optimized conformer geometries, torsion fingerprint deviations (TFD), and improved relative conformer energetics (ΔΔE). We present a variety of benchmarks for these metrics against our previous force fields as well as in some cases other small molecule force fields. Sage also demonstrates improved performance in estimating physical properties, including comparison against experimental data from various thermodynamic databases for small molecule properties such as ΔH(mix), ρ(x), ΔG(solv), and ΔG(trans). Additionally, we benchmarked against protein–ligand binding free energies (ΔG(bind)), where Sage yields results statistically similar to previous force fields. All the data is made publicly available along with complete details on how to reproduce the training results at https://github.com/openforcefield/openff-sage. American Chemical Society 2023-05-11 /pmc/articles/PMC10269353/ /pubmed/37167319 http://dx.doi.org/10.1021/acs.jctc.3c00039 Text en © 2023 The Authors. Published by American Chemical Society https://creativecommons.org/licenses/by/4.0/Permits the broadest form of re-use including for commercial purposes, provided that author attribution and integrity are maintained (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Boothroyd, Simon
Behara, Pavan Kumar
Madin, Owen C.
Hahn, David F.
Jang, Hyesu
Gapsys, Vytautas
Wagner, Jeffrey R.
Horton, Joshua T.
Dotson, David L.
Thompson, Matthew W.
Maat, Jessica
Gokey, Trevor
Wang, Lee-Ping
Cole, Daniel J.
Gilson, Michael K.
Chodera, John D.
Bayly, Christopher I.
Shirts, Michael R.
Mobley, David L.
Development and Benchmarking of Open Force Field 2.0.0: The Sage Small Molecule Force Field
title Development and Benchmarking of Open Force Field 2.0.0: The Sage Small Molecule Force Field
title_full Development and Benchmarking of Open Force Field 2.0.0: The Sage Small Molecule Force Field
title_fullStr Development and Benchmarking of Open Force Field 2.0.0: The Sage Small Molecule Force Field
title_full_unstemmed Development and Benchmarking of Open Force Field 2.0.0: The Sage Small Molecule Force Field
title_short Development and Benchmarking of Open Force Field 2.0.0: The Sage Small Molecule Force Field
title_sort development and benchmarking of open force field 2.0.0: the sage small molecule force field
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10269353/
https://www.ncbi.nlm.nih.gov/pubmed/37167319
http://dx.doi.org/10.1021/acs.jctc.3c00039
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