A semiempirical method optimized for modeling proteins.

ABSTRACT:

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,

SUBMITTER: Stewart JJP 

PROVIDER: S-EPMC10444645 | biostudies-literature | 2023 Aug

REPOSITORIES: biostudies-literature