Interplay of I-TASSER and QUARK for template-based and ab initio protein structure prediction in CASP10.

ABSTRACT: We develop and test a new pipeline in CASP10 to predict protein structures based on an interplay of I-TASSER and QUARK for both free-modeling (FM) and template-based modeling (TBM) targets. The most noteworthy observation is that sorting through the threading template pool using the QUARK-based ab initio models as probes allows the detection of distant-homology templates which might be ignored by the traditional sequence profile-based threading alignment algorithms. Further template assembly refinement by I-TASSER resulted in successful folding of two medium-sized FM targets with >150 residues. For TBM, the multiple threading alignments from LOMETS are, for the first time, incorporated into the ab initio QUARK simulations, which were further refined by I-TASSER assembly refinement. Compare

SUBMITTER: Zhang Y 

PROVIDER: S-EPMC4067246 | biostudies-literature | 2014 Feb

REPOSITORIES: biostudies-literature