REMO: A new protocol to refine full atomic protein models from C-alpha traces by optimizing hydrogen-bonding networks.

ABSTRACT: Protein structure prediction approaches usually perform modeling simulations based on reduced representation of protein structures. For biological utilizations, it is an important step to construct full atomic models from the reduced structure decoys. Most of the current full atomic model reconstruction procedures have defects which either could not completely remove the steric clashes among backbone atoms or generate final atomic models with worse topology similarity relative to the native structures than the reduced models. In this work, we develop a new protocol, called REMO, to generate full atomic protein models by optimizing the hydrogen-bonding network with basic fragments matched from a newly constructed backbone isomer library of solved protein structures. The algorithm is benchma

SUBMITTER: Li Y 

PROVIDER: S-EPMC2771173 | biostudies-literature | 2009 Aug

REPOSITORIES: biostudies-literature