Automated Servers: Prediction Report

Prediction of CASP6 structures using automated robetta protocols†

  1. Dylan Chivian1,‡,
  2. David E. Kim1,‡,
  3. Lars Malmström1,
  4. Jack Schonbrun2,
  5. Carol A. Rohl3,
  6. David Baker1,2,*

Article first published online: 26 SEP 2005

DOI: 10.1002/prot.20733

Issue

Proteins: Structure, Function, and Bioinformatics

Proteins: Structure, Function, and Bioinformatics

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

Volume 61, Issue Supplement 7, pages 157–166, 2005

Additional Information

How to Cite

Chivian, D., Kim, D. E., Malmström, L., Schonbrun, J., Rohl, C. A. and Baker, D. (2005), Prediction of CASP6 structures using automated robetta protocols. Proteins: Structure, Function, and Bioinformatics, 61: 157–166. doi: 10.1002/prot.20733

Author Information

  1. 1

    Department of Biochemistry, University of Washington, Seattle, Washington

  2. 2

    Howard Hughes Medical Institute, Seattle, Washington

  3. 3

    Department of Biomolecular Engineering, University of California, Santa Cruz, California

  1. ‡

    Dylan Chivian and David E. Kim contributed equally to this paper.

*Dept. of Biochemistry and HHMI, University of Washington, Box 357350, Seattle, Washington 98195

  1. †

    This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version.

Publication History

  1. Issue published online: 29 DEC 2005
  2. Article first published online: 26 SEP 2005
  3. Manuscript Accepted: 24 JUN 2005
  4. Manuscript Received: 15 APR 2005

Funded by

  • NIH/NIGMS SGPP
  • HHMI

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Keywords:

  • Rosetta;
  • fragment assembly;
  • de novo modeling;
  • homology modeling;
  • parametric alignment ensemble

Abstract

The Robetta server and revised automatic protocols were used to predict structures for CASP6 targets. Robetta is a publicly available protein structure prediction server (http://robetta.bakerlab.org/ that uses the Rosetta de novo and homology modeling structure prediction methods. We incorporated some of the lessons learned in the CASP5 experiment into the server prior to participating in CASP6. We additionally tested new ideas that were amenable to full-automation with an eye toward improving the server. We find that the Robetta server shows the greatest promise for the more challenging targets. The most significant finding from CASP5, that automated protocols can be roughly comparable in ability with the better human-intervention predictors, is repeated here in CASP6. Proteins 2005;Suppl 7:157–166. © 2005 Wiley-Liss, Inc.

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