Recovering physical potentials from a model protein databank.

ABSTRACT: Knowledge-based approaches frequently employ empirical relations to determine effective potentials for coarse-grained protein models directly from protein databank structures. Although these approaches have enjoyed considerable success and widespread popularity in computational protein science, their fundamental basis has been widely questioned. It is well established that conventional knowledge-based approaches do not correctly treat many-body correlations between amino acids. Moreover, the physical significance of potentials determined by using structural statistics from different proteins has remained obscure. In the present work, we address both of these concerns by introducing and demonstrating a theory for calculating transferable potentials directly from a databank of protein struct

SUBMITTER: Mullinax JW 

PROVIDER: S-EPMC2993375 | biostudies-literature | 2010 Nov

REPOSITORIES: biostudies-literature