Stochastic reconstruction of protein structures from effective connectivity profiles.

ABSTRACT: We discuss a stochastic approach for reconstructing the native structures of proteins from the knowledge of the "effective connectivity", which is a one-dimensional structural profile constructed as a linear combination of the eigenvectors of the contact map of the target structure. The structural profile is used to bias a search of the conformational space towards the target structure in a Monte Carlo scheme operating on a Calpha-chain of uniform, finite thickness. Structure information thus enters the folding dynamics via the effective connectivity, but the interaction is not restricted to pairs of amino acids that form native contacts, resulting in a free energy landscape which does not rely on the assumption of minimal frustration. Moreover, effective connectivity vectors can be predic

SUBMITTER: Wolff K 

PROVIDER: S-EPMC2666633 | biostudies-literature | 2008 Nov

REPOSITORIES: biostudies-literature