Integration of QUARK and I-TASSER for Ab Initio Protein Structure Prediction in CASP11.

ABSTRACT: We tested two pipelines developed for template-free protein structure prediction in the CASP11 experiment. First, the QUARK pipeline constructs structure models by reassembling fragments of continuously distributed lengths excised from unrelated proteins. Five free-modeling (FM) targets have the model successfully constructed by QUARK with a TM-score above 0.4, including the first model of T0837-D1, which has a TM-score = 0.736 and RMSD = 2.9 Å to the native. Detailed analysis showed that the success is partly attributed to the high-resolution contact map prediction derived from fragment-based distance-profiles, which are mainly located between regular secondary structure elements and loops/turns and help guide the orientation of secondary structure assembly. In the Zhang-Server pipeline,

SUBMITTER: Zhang W 

PROVIDER: S-EPMC4792809 | biostudies-literature | 2016 Sep

REPOSITORIES: biostudies-literature