Optimized atomic statistical potentials: assessment of protein interfaces and loops.

ABSTRACT:

Motivation

Statistical potentials have been widely used for modeling whole proteins and their parts (e.g. sidechains and loops) as well as interactions between proteins, nucleic acids and small molecules. Here, we formulate the statistical potentials entirely within a statistical framework, avoiding questionable statistical mechanical assumptions and approximations, including a definition of the reference state.

Results

We derive a general Bayesian framework for inferring statistically optimized atomic potentials (SOAP) in which the reference state is replaced with data-driven 'recovery' functions. Moreover, we restrain the relative orientation between two covalent bonds instead of a simple distance between two atoms, in an effort to capture orientation-dependent interaction

SUBMITTER: Dong GQ 

PROVIDER: S-EPMC3842762 | biostudies-literature | 2013 Dec

REPOSITORIES: biostudies-literature