BCL::Fold--de novo prediction of complex and large protein topologies by assembly of secondary structure elements.

ABSTRACT: Computational de novo protein structure prediction is limited to small proteins of simple topology. The present work explores an approach to extend beyond the current limitations through assembling protein topologies from idealized α-helices and β-strands. The algorithm performs a Monte Carlo Metropolis simulated annealing folding simulation. It optimizes a knowledge-based potential that analyzes radius of gyration, β-strand pairing, secondary structure element (SSE) packing, amino acid pair distance, amino acid environment, contact order, secondary structure prediction agreement and loop closure. Discontinuation of the protein chain favors sampling of non-local contacts and thereby creation of complex protein topologies. The folding simulation is accelerated through exclusion of flexible

SUBMITTER: Karakas M 

PROVIDER: S-EPMC3500284 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature