Combining Force Fields and Neural Networks for an Accurate Representation of Bonded Interactions.

Autor:	Kamath G; InterX Inc. (a subsidiary of NeoTX Therapeutics LTD), 805 Allston Way, Berkeley, California 94710, United States., Illarionov A; InterX Inc. (a subsidiary of NeoTX Therapeutics LTD), 805 Allston Way, Berkeley, California 94710, United States., Sakipov S; InterX Inc. (a subsidiary of NeoTX Therapeutics LTD), 805 Allston Way, Berkeley, California 94710, United States., Pereyaslavets L; InterX Inc. (a subsidiary of NeoTX Therapeutics LTD), 805 Allston Way, Berkeley, California 94710, United States., Kurnikov IV; InterX Inc. (a subsidiary of NeoTX Therapeutics LTD), 805 Allston Way, Berkeley, California 94710, United States., Butin O; InterX Inc. (a subsidiary of NeoTX Therapeutics LTD), 805 Allston Way, Berkeley, California 94710, United States., Voronina E; InterX Inc. (a subsidiary of NeoTX Therapeutics LTD), 805 Allston Way, Berkeley, California 94710, United States.; Lomonosov MSU, Skobeltsyn Institute of Nuclear Physics, Moscow 119991, Russia., Ivahnenko I; InterX Inc. (a subsidiary of NeoTX Therapeutics LTD), 805 Allston Way, Berkeley, California 94710, United States., Leontyev I; InterX Inc. (a subsidiary of NeoTX Therapeutics LTD), 805 Allston Way, Berkeley, California 94710, United States., Nawrocki G; InterX Inc. (a subsidiary of NeoTX Therapeutics LTD), 805 Allston Way, Berkeley, California 94710, United States., Darkhovskiy M; InterX Inc. (a subsidiary of NeoTX Therapeutics LTD), 805 Allston Way, Berkeley, California 94710, United States., Olevanov M; InterX Inc. (a subsidiary of NeoTX Therapeutics LTD), 805 Allston Way, Berkeley, California 94710, United States.; Department of Physics, Lomonosov MSU, Moscow 119991, Russia., Cherniavskyi YK; InterX Inc. (a subsidiary of NeoTX Therapeutics LTD), 805 Allston Way, Berkeley, California 94710, United States., Lock C; InterX Inc. (a subsidiary of NeoTX Therapeutics LTD), 805 Allston Way, Berkeley, California 94710, United States.; Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Palo Alto, California 94304, United States., Greenslade S; InterX Inc. (a subsidiary of NeoTX Therapeutics LTD), 805 Allston Way, Berkeley, California 94710, United States., Chen Y; InterX Inc. (a subsidiary of NeoTX Therapeutics LTD), 805 Allston Way, Berkeley, California 94710, United States., Kornberg RD; Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94304, United States., Levitt M; Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94304, United States., Fain B; InterX Inc. (a subsidiary of NeoTX Therapeutics LTD), 805 Allston Way, Berkeley, California 94710, United States.
Jazyk:	angličtina
Zdroj:	The journal of physical chemistry. A [J Phys Chem A] 2024 Feb 01; Vol. 128 (4), pp. 807-812. Date of Electronic Publication: 2024 Jan 17.
DOI:	10.1021/acs.jpca.3c07598
Abstrakt:	We present a formalism of a neural network encoding bonded interactions in molecules. This intramolecular encoding is consistent with the models of intermolecular interactions previously designed by this group. Variants of the encoding fed into a corresponding neural network may be used to economically improve the representation of torsional degrees of freedom in any force field. We test the accuracy of the reproduction of the ab initio potential energy surface on a set of conformations of two dipeptides, methyl-capped ALA and ASP, in several scenarios. The encoding, either alone or in conjunction with an analytical potential, improves agreement with ab initio energies that are on par with those of other neural network-based potentials. Using the encoding and neural nets in tandem with an analytical model places the agreements firmly within "chemical accuracy" of ±0.5 kcal/mol.
Databáze:	MEDLINE
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