The Development and Applications of Models for Molecular Problems

Abstract

We have proposed revisions for a pre-existing homology-based protein structure modeling tool interfaced with the CHARMM program in order to solve its derivative discontinuity problem, to suggest a simplified form of restraining functions, and to optimize several parameters. We have also developed new statistical potential energy functions for various protein torsion angle combinations. The utilities of the modeling tools and the statistical functions are examined for a large number of protein targets used in critical assessment of protein structure prediction (CASP). For excited state problems, multireference quantum chemical treatment, based on complete active space self-consistent field (CASSCF) method, has been applied to several model systems.