Quantum chemical calculation dataset for representative protein folds by the fragment molecular orbital method.
Journal
Scientific data
ISSN: 2052-4463
Titre abrégé: Sci Data
Pays: England
ID NLM: 101640192
Informations de publication
Date de publication:
23 Oct 2024
23 Oct 2024
Historique:
received:
02
07
2024
accepted:
11
10
2024
medline:
24
10
2024
pubmed:
24
10
2024
entrez:
24
10
2024
Statut:
epublish
Résumé
The function of a biomacromolecule is not only determined by its three-dimensional structure but also by its electronic state. Quantum chemical calculations are promising non-empirical methods available for determining the electronic state of a given structure. In this study, we used the fragment molecular orbital (FMO) method, which applies to biopolymers such as proteins, to provide physicochemical property values on representative structures in the SCOP2 database of protein families, a subset of the Protein Data Bank. Our dataset was constructed by over 5,000 protein structures, including over 200 million inter-fragment interaction energies (IFIEs) and their energy components obtained by pair interaction energy decomposition analysis (PIEDA) using FMO-MP2/6-31 G*. Moreover, three basis sets, 6-31 G*, 6-31 G**, and cc-pVDZ, were used for the FMO calculations of each structure, making it possible to compare the energies obtained with different basis functions for the same fragment pair. The total data size is approximately 6.7 GB. Our dataset will be useful for functional analyses and machine learning based on the physicochemical property values of proteins.
Identifiants
pubmed: 39443514
doi: 10.1038/s41597-024-03999-2
pii: 10.1038/s41597-024-03999-2
doi:
Substances chimiques
Proteins
0
Types de publication
Dataset
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
1164Subventions
Organisme : Japan Agency for Medical Research and Development (AMED)
ID : JP23ama121030
Organisme : Japan Agency for Medical Research and Development (AMED)
ID : JP23ama121030
Organisme : Japan Agency for Medical Research and Development (AMED)
ID : JP23ama121030
Organisme : Japan Agency for Medical Research and Development (AMED)
ID : JP23ama121030
Organisme : Japan Agency for Medical Research and Development (AMED)
ID : JP23ama121030
Organisme : MEXT | Japan Society for the Promotion of Science (JSPS)
ID : 23K11320
Informations de copyright
© 2024. The Author(s).
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