ArticleProteins2016
Template-based protein structure prediction in CASP11 and retrospect of I-TASSER in the last decade.
Article in Proteins, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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34 citing papers in PubMed.
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- A practical guide to large-scale docking.Nature protocols · 2021Review
- Deep Learning-Based Advances in Protein Structure Prediction.International journal of molecular sciences · 2021Review
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- Structural and functional divergence of GDAP1 from the glutathione S-transferase superfamily.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2020Article
- Comparative evaluation of structure and characteristic of peptidyl-prolyl cis-trans isomerase proteins and their function in Salmonella Typhimurium stress responses and virulence.Folia microbiologica · 2020Article
- Structural Comparison of the SARS CoV 2 Spike Protein Relative to Other Human-Infecting Coronaviruses.Frontiers in medicine · 2020Article
- Computational Analysis ofCancer informatics · 2020Article
- Ranking near-native candidate protein structures via random forest classification.BMC bioinformatics · 2019Article
- In silico prediction of prolactin molecules as a tool for equine genomics reproduction.Molecular diversity · 2019Article
- Modeling of Disordered Protein Structures Using Monte Carlo Simulations and Knowledge-Based Statistical Force Fields.International journal of molecular sciences · 2019Review
- Repository of Enriched Structures of Proteins Involved in the Red Blood Cell Environment (RESPIRE).PloS one · 2019Article
- Experimental accuracy in protein structure refinement via molecular dynamics simulations.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
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10 authors.
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Abstract
We report the structure prediction results of a new composite pipeline for template-based modeling (TBM) in the 11th CASP experiment. Starting from multiple structure templates identified by LOMETS based meta-threading programs, the QUARK ab initio folding program is extended to generate initial full-length models under strong constraints from template alignments. The final atomic models are then constructed by I-TASSER based fragment reassembly simulations, followed by the fragment-guided molecular dynamic simulation and the MQAP-based model selection. It was found that the inclusion of QUARK-TBM simulations as an intermediate modeling step could help improve the quality of the I-TASSER models for both Easy and Hard TBM targets. Overall, the average TM-score of the first I-TASSER model is 12% higher than that of the best LOMETS templates, with the RMSD in the same threading-aligned regions reduced from 5.8 to 4.7 Å. Nevertheless, there are nearly 18% of TBM domains with the templates deteriorated by the structure assembly pipeline, which may be attributed to the errors of secondary structure and domain orientation predictions that propagate through and degrade the procedures of template identification and final model selections. To examine the record of progress, we made a retrospective report of the I-TASSER pipeline in the last five CASP experiments (CASP7-11). The data show no clear progress of the LOMETS threading programs over PSI-BLAST; but obvious progress on structural improvement relative to threading templates was witnessed in recent CASP experiments, which is probably attributed to the integration of the extended ab initio folding simulation with the threading assembly pipeline and the introduction of atomic-level structure refinements following the reduced modeling simulations. Proteins 2016; 84(Suppl 1):233-246. © 2015 Wiley Periodicals, Inc.
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