A semiempirical method optimized for modeling proteins

• Published in: Journal of molecular modeling 2023-09, Vol.29 (9), p.284-284, Article 284
• Main Authors: Stewart, James J. P., Stewart, Anna C.
• Format: Article
• Language: English
• Subjects: Biochemistry; Characterization and Evaluation of Materials; Chemistry; Chemistry and Materials Science; Computer Appl. in Life Sciences; Computer Applications in Chemistry; Errors; Heat of formation; Hydrogen bonding; Modelling; Molecular Medicine; Original Paper; Proteins; Quantum theory; Theoretical and Computational Chemistry
• ISSN: 1610-2940; 0948-5023
• DOI: 10.1007/s00894-023-05695-1

Context 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. Methods 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.