Information-theoretic analysis of the reference state in contact potentials used for protein structure prediction.

ABSTRACT: Using information-theoretic concepts, we examine the role of the reference state, a crucial component of empirical potential functions, in protein fold recognition. We derive an information-based connection between the probability distribution functions of the reference state and those that characterize the decoy set used in threading. In examining commonly used contact reference states, we find that the quasi-chemical approximation is informatically superior to other variant models designed to include characteristics of real protein chains, such as finite length and variable amino acid composition from protein to protein. We observe that in these variant models, the total divergence, the operative function that quantifies discrimination, decreases along with threading performance. We find

SUBMITTER: Solis AD 

PROVIDER: S-EPMC2841228 | biostudies-literature | 2010 May

REPOSITORIES: biostudies-literature