Template‐based protein structure prediction in CASP11 and retrospect of I‐TASSER in the last decade

• DOI: 10.1002/prot.24918
• Publication Date: 2015-09-07T23:45:09Z
• Authors: Jianyi Yang; Wenxuan Zhang; Baoji He; Sara Elizabeth Wa...; Hongjiu Zhang; Brandon Govindarajoo; Jouko Virtanen; Zhidong Xue; Hong‐Bin Shen; Yang Zhang
• Keywords: CASP; Threading (protein sequence); Template; Fragment (logic); Folding (DSP implementation)

We report the structure prediction results of a new composite pipeline for template-based modeling (TBM) in 11th CASP experiment. Starting from multiple templates identified by LOMETS based meta-threading programs, QUARK ab initio folding program is extended to generate initial full-length models under strong constraints template alignments. The final atomic are then constructed I-TASSER fragment reassembly simulations, followed fragment-guided molecular dynamic simulation and MQAP-based model selection. It was found that inclusion QUARK-TBM simulations as an intermediate step could help improve quality both Easy Hard TBM targets. Overall, average TM-score first 12% higher than best templates, with RMSD same threading-aligned regions reduced 5.8 4.7 Å. Nevertheless, there nearly 18% domains deteriorated assembly pipeline, which may be attributed errors secondary domain orientation predictions propagate through degrade procedures identification selections. To examine record progress, we made retrospective last five experiments (CASP7-11). data show no clear progress threading programs over PSI-BLAST; but obvious on structural improvement relative witnessed recent experiments, probably integration introduction atomic-level refinements following simulations. Proteins 2016; 84(Suppl 1):233-246. © 2015 Wiley Periodicals, Inc.