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SPICE, A Dataset of Drug-like Molecules and Peptides for Training Machine Learning Potentials

Machine learning potentials are an important tool for molecular simulation, but their development is held back by a shortage of high quality datasets to train them on. We describe the SPICE dataset, a new quantum chemistry dataset for training potentials relevant to simulating drug-like small molecu...

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Autores principales: Eastman, Peter, Behara, Pavan Kumar, Dotson, David L., Galvelis, Raimondas, Herr, John E., Horton, Josh T., Mao, Yuezhi, Chodera, John D., Pritchard, Benjamin P., Wang, Yuanqing, De Fabritiis, Gianni, Markland, Thomas E.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9813265/
https://www.ncbi.nlm.nih.gov/pubmed/36599873
http://dx.doi.org/10.1038/s41597-022-01882-6
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author Eastman, Peter
Behara, Pavan Kumar
Dotson, David L.
Galvelis, Raimondas
Herr, John E.
Horton, Josh T.
Mao, Yuezhi
Chodera, John D.
Pritchard, Benjamin P.
Wang, Yuanqing
De Fabritiis, Gianni
Markland, Thomas E.
author_facet Eastman, Peter
Behara, Pavan Kumar
Dotson, David L.
Galvelis, Raimondas
Herr, John E.
Horton, Josh T.
Mao, Yuezhi
Chodera, John D.
Pritchard, Benjamin P.
Wang, Yuanqing
De Fabritiis, Gianni
Markland, Thomas E.
author_sort Eastman, Peter
collection PubMed
description Machine learning potentials are an important tool for molecular simulation, but their development is held back by a shortage of high quality datasets to train them on. We describe the SPICE dataset, a new quantum chemistry dataset for training potentials relevant to simulating drug-like small molecules interacting with proteins. It contains over 1.1 million conformations for a diverse set of small molecules, dimers, dipeptides, and solvated amino acids. It includes 15 elements, charged and uncharged molecules, and a wide range of covalent and non-covalent interactions. It provides both forces and energies calculated at the ωB97M-D3(BJ)/def2-TZVPPD level of theory, along with other useful quantities such as multipole moments and bond orders. We train a set of machine learning potentials on it and demonstrate that they can achieve chemical accuracy across a broad region of chemical space. It can serve as a valuable resource for the creation of transferable, ready to use potential functions for use in molecular simulations.
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spelling pubmed-98132652023-01-06 SPICE, A Dataset of Drug-like Molecules and Peptides for Training Machine Learning Potentials Eastman, Peter Behara, Pavan Kumar Dotson, David L. Galvelis, Raimondas Herr, John E. Horton, Josh T. Mao, Yuezhi Chodera, John D. Pritchard, Benjamin P. Wang, Yuanqing De Fabritiis, Gianni Markland, Thomas E. Sci Data Data Descriptor Machine learning potentials are an important tool for molecular simulation, but their development is held back by a shortage of high quality datasets to train them on. We describe the SPICE dataset, a new quantum chemistry dataset for training potentials relevant to simulating drug-like small molecules interacting with proteins. It contains over 1.1 million conformations for a diverse set of small molecules, dimers, dipeptides, and solvated amino acids. It includes 15 elements, charged and uncharged molecules, and a wide range of covalent and non-covalent interactions. It provides both forces and energies calculated at the ωB97M-D3(BJ)/def2-TZVPPD level of theory, along with other useful quantities such as multipole moments and bond orders. We train a set of machine learning potentials on it and demonstrate that they can achieve chemical accuracy across a broad region of chemical space. It can serve as a valuable resource for the creation of transferable, ready to use potential functions for use in molecular simulations. Nature Publishing Group UK 2023-01-04 /pmc/articles/PMC9813265/ /pubmed/36599873 http://dx.doi.org/10.1038/s41597-022-01882-6 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Data Descriptor
Eastman, Peter
Behara, Pavan Kumar
Dotson, David L.
Galvelis, Raimondas
Herr, John E.
Horton, Josh T.
Mao, Yuezhi
Chodera, John D.
Pritchard, Benjamin P.
Wang, Yuanqing
De Fabritiis, Gianni
Markland, Thomas E.
SPICE, A Dataset of Drug-like Molecules and Peptides for Training Machine Learning Potentials
title SPICE, A Dataset of Drug-like Molecules and Peptides for Training Machine Learning Potentials
title_full SPICE, A Dataset of Drug-like Molecules and Peptides for Training Machine Learning Potentials
title_fullStr SPICE, A Dataset of Drug-like Molecules and Peptides for Training Machine Learning Potentials
title_full_unstemmed SPICE, A Dataset of Drug-like Molecules and Peptides for Training Machine Learning Potentials
title_short SPICE, A Dataset of Drug-like Molecules and Peptides for Training Machine Learning Potentials
title_sort spice, a dataset of drug-like molecules and peptides for training machine learning potentials
topic Data Descriptor
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9813265/
https://www.ncbi.nlm.nih.gov/pubmed/36599873
http://dx.doi.org/10.1038/s41597-022-01882-6
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