Predictions from Automatic Servers

Automated prediction of CASP-5 structures using the Robetta server

  1. Dylan Chivian1,
  2. David E. Kim1,
  3. Lars Malmström1,
  4. Philip Bradley1,
  5. Timothy Robertson1,
  6. Paul Murphy1,
  7. Charles E.M. Strauss2,
  8. Richard Bonneau3,
  9. Carol A. Rohl4,
  10. David Baker1,*

Article first published online: 15 OCT 2003

DOI: 10.1002/prot.10529

Issue

Proteins: Structure, Function, and Bioinformatics

Proteins: Structure, Function, and Bioinformatics

Supplement: Fifth Meeting on the Critical Assessment of Techniques for Protein Structure Prediction

Volume 53, Issue Supplement 6, pages 524–533, 2003

Additional Information

How to Cite

Chivian, D., Kim, D. E., Malmström, L., Bradley, P., Robertson, T., Murphy, P., Strauss, C. E., Bonneau, R., Rohl, C. A. and Baker, D. (2003), Automated prediction of CASP-5 structures using the Robetta server. Proteins: Structure, Function, and Bioinformatics, 53: 524–533. doi: 10.1002/prot.10529

Author Information

  1. 1

    University of Washington, Seattle, Washington

  2. 2

    Los Alamos National Laboratory, Los Alamos, New Mexico

  3. 3

    Institute for Systems Biology, Seattle, Washington

  4. 4

    University of California, Santa Cruz, California

*Department of Biochemistry and HHMI, University of Washington, Box 357350, Seattle, WA 98195

Publication History

  1. Issue published online: 15 OCT 2003
  2. Article first published online: 15 OCT 2003
  3. Manuscript Accepted: 23 JUN 2003
  4. Manuscript Received: 22 FEB 2003

Funded by

  • Burroughs-Wellcome Fund
  • NIH
  • HHMI

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Keywords:

  • automated protein structure prediction server;
  • CASP;
  • CAFASP;
  • rosetta;
  • fragment insertion;
  • fragment assembly;
  • ab initiomodeling;
  • de novomodeling;
  • template-based modeling;
  • domain parsing;
  • homology modeling;
  • comparative modeling;
  • sequence alignment

Abstract

Robetta is a fully automated protein structure prediction server that uses the Rosetta fragment-insertion method. It combines template-based and de novo structure prediction methods in an attempt to produce high quality models that cover every residue of a submitted sequence. The first step in the procedure is the automatic detection of the locations of domains and selection of the appropriate modeling protocol for each domain. For domains matched to a homolog with an experimentally characterized structure by PSI-BLAST or Pcons2, Robetta uses a new alignment method, called K*Sync, to align the query sequence onto the parent structure. It then models the variable regions by allowing them to explore conformational space with fragments in fashion similar to the de novo protocol, but in the context of the template. When no structural homolog is available, domains are modeled with the Rosetta de novo protocol, which allows the full length of the domain to explore conformational space via fragment-insertion, producing a large decoy ensemble from which the final models are selected. The Robetta server produced quite reasonable predictions for targets in the recent CASP-5 and CAFASP-3 experiments, some of which were at the level of the best human predictions. Proteins 2003;53:524–533. © 2003 Wiley-Liss, Inc.

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