Explicit orientation dependence in empirical potentials and its significance to side-chain modeling.

ABSTRACT: Protein structure modeling and prediction have important applications throughout the biological sciences, from the design of pharmaceuticals to the elucidation of enzyme mechanisms. At the core of most protein modeling is an energy function, the minimum of which represents the free energy "cost" for forming a correct protein structure. The most commonly used energy functions are knowledge-based statistical potential functions; that is, they are empirically derived from statistical analysis of a set of high-resolution protein structures. When that kind of potential function is constructed, the anisotropic orientation dependence between the interacting groups is a critical component for accurately representing key molecular interactions, such as those involved in protein side-chain packing.

SUBMITTER: Ma J 

PROVIDER: S-EPMC2728797 | biostudies-literature | 2009 Aug

REPOSITORIES: biostudies-literature