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Proteins. 2019 Dec;87(12):1241-1248. doi: 10.1002/prot.25808. Epub 2019 Oct 1.

Template-based modeling by ClusPro in CASP13 and the potential for using co-evolutionary information in docking.

Author information

1
Department of Biomedical Engineering, Boston University, Boston, Massachusetts.
2
Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York.
3
Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York.
4
Moscow Institute of Physics and Technology, Dolgoprudny, Russia.
5
Department of Biochemistry, University of Washington, Seattle, Washington.
6
Institute for Protein Design, University of Washington, Seattle, Washington.
7
Center for Systems Biology, Harvard University, Cambridge, Massachusetts.
8
Howard Hughes Medical Institute, University of Washington, Seattle, Washington.
9
Department of Chemistry, Boston University, Boston, Massachusetts.

Abstract

As a participant in the joint CASP13-CAPRI46 assessment, the ClusPro server debuted its new template-based modeling functionality. The addition of this feature, called ClusPro TBM, was motivated by the previous CASP-CAPRI assessments and by the proven ability of template-based methods to produce higher-quality models, provided templates are available. In prior assessments, ClusPro submissions consisted of models that were produced via free docking of pre-generated homology models. This method was successful in terms of the number of acceptable predictions across targets; however, analysis of results showed that purely template-based methods produced a substantially higher number of medium-quality models for targets for which there were good templates available. The addition of template-based modeling has expanded ClusPro's ability to produce higher accuracy predictions, primarily for homomeric but also for some heteromeric targets. Here we review the newest additions to the ClusPro web server and discuss examples of CASP-CAPRI targets that continue to drive further development. We also describe ongoing work not yet implemented in the server. This includes the development of methods to improve template-based models and the use of co-evolutionary information for data-assisted free docking.

KEYWORDS:

homology modeling; method development; modeling of protein complexes; protein-protein interaction; template-based

PMID:
31444975
DOI:
10.1002/prot.25808

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