A semiempirical method optimized for modeling proteins.
MOPAC
PM6-ORG
parameterization
proteins
reference data
semiempirical
Journal
Journal of molecular modeling
ISSN: 0948-5023
Titre abrégé: J Mol Model
Pays: Germany
ID NLM: 9806569
Informations de publication
Date de publication:
22 Aug 2023
22 Aug 2023
Historique:
received:
03
08
2023
accepted:
15
08
2023
medline:
24
8
2023
pubmed:
23
8
2023
entrez:
23
8
2023
Statut:
epublish
Résumé
In recent years, semiempirical methods such as PM6, PM6-D3H4, and PM7 have been increasingly used for modeling proteins, in particular enzymes. These methods were designed for more general use, and consequently were not optimized for studying proteins. Because of this, various specific errors have been found that could potentially cast doubt on the validity of these methods for modeling phenomena of biochemical interest such as enzyme catalytic mechanisms and protein-ligand interactions. To correct these and other errors, a new method specifically designed for use in organic and biochemical modeling has been developed. Two alterations were made to the procedures used in developing the earlier PMx methods. A minor change was made to the theoretical framework, which affected only the non-quantum theory interatomic interaction function, while the major change involved changing the training set for optimizing parameters, moving the focus to systems of biochemical significance. This involved both the selection of reference data and the weighting factors, i.e., the relative importance that the various data were given. As a result of this change of focus, the accuracy in prediction of heats of formation, hydrogen bonding, and geometric quantities relating to non-covalent interactions in proteins was improved significantly.
Identifiants
pubmed: 37608199
doi: 10.1007/s00894-023-05695-1
pii: 10.1007/s00894-023-05695-1
pmc: PMC10444645
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
284Informations de copyright
© 2023. The Author(s).
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