BCL::MP-fold: folding membrane proteins through assembly of transmembrane helices.

ABSTRACT: Membrane protein structure determination remains a challenging endeavor. Computational methods that predict membrane protein structure from sequence can potentially aid structure determination for such difficult target proteins. The de novo protein structure prediction method BCL::Fold rapidly assembles secondary structure elements into three-dimensional models. Here, we describe modifications to the algorithm, named BCL::MP-Fold, in order to simulate membrane protein folding. Models are built into a static membrane object and are evaluated using a knowledge-based energy potential, which has been modified to account for the membrane environment. Additionally, a symmetry folding mode allows for the prediction of obligate homomultimers, a common property among membrane proteins. In a benchma

SUBMITTER: Weiner BE 

PROVIDER: S-EPMC3738745 | biostudies-literature | 2013 Jul

REPOSITORIES: biostudies-literature