Prediction Report

Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home

  1. Rhiju Das1,2,†,
  2. Bin Qian1,†,
  3. Srivatsan Raman1,3,
  4. Robert Vernon1,
  5. James Thompson1,2,
  6. Philip Bradley1,
  7. Sagar Khare1,
  8. Michael D. Tyka1,
  9. Divya Bhat1,2,
  10. Dylan Chivian4,
  11. David E. Kim1,
  12. William H. Sheffler1,2,
  13. Lars Malmström1,
  14. Andrew M. Wollacott1,
  15. Chu Wang1,
  16. Ingemar Andre1,
  17. David Baker1,2,3,*

Article first published online: 25 SEP 2007

DOI: 10.1002/prot.21636

Issue

Proteins: Structure, Function, and Bioinformatics

Proteins: Structure, Function, and Bioinformatics

Supplement: Proteins

Volume 69, Issue Supplement S8, pages 118–128, 2007

Additional Information

How to Cite

Das, R., Qian, B., Raman, S., Vernon, R., Thompson, J., Bradley, P., Khare, S., Tyka, M. D., Bhat, D., Chivian, D., Kim, D. E., Sheffler, W. H., Malmström, L., Wollacott, A. M., Wang, C., Andre, I. and Baker, D. (2007), Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home. Proteins: Structure, Function, and Bioinformatics, 69: 118–128. doi: 10.1002/prot.21636

Author Information

  1. 1

    Department of Biochemistry, University of Washington, Seattle, Washington 98195

  2. 2

    Department of Genome Sciences, University of Washington, Seattle, Washington 98195

  3. 3

    Department of Biomolecular Structure and Design, University of Washington, Seattle, Washington 98195

  4. 4

    Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720

  1. †

    Rhiju Das and Bin Qian contributed equally to this work.

*Department of Biochemistry, University of Washington, J Wing, Health Sciences Building, Box 357350, Seattle, WA 98195

Publication History

  1. Issue published online: 30 OCT 2007
  2. Article first published online: 25 SEP 2007
  3. Manuscript Accepted: 11 MAY 2007
  4. Manuscript Revised: 7 MAY 2007
  5. Manuscript Received: 28 FEB 2007

Funded by

  • National Institute of General Medical Sciences
  • National Institutes of Health. Grant Number: P20 GM76222
  • Interdisciplinary Training in Genomic Sciences. Grant Number: T32 HG00035
  • Howard Hughes Medical Institute
  • American Leukemia and Lymphoma Society

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Keywords:

  • protein structure prediction;
  • fragment insertion;
  • Rosetta;
  • CASP;
  • all-atom refinement;
  • template-based modeling;
  • free modeling

Abstract

We describe predictions made using the Rosetta structure prediction methodology for both template-based modeling and free modeling categories in the Seventh Critical Assessment of Techniques for Protein Structure Prediction. For the first time, aggressive sampling and all-atom refinement could be carried out for the majority of targets, an advance enabled by the Rosetta@home distributed computing network. Template-based modeling predictions using an iterative refinement algorithm improved over the best existing templates for the majority of proteins with less than 200 residues. Free modeling methods gave near-atomic accuracy predictions for several targets under 100 residues from all secondary structure classes. These results indicate that refinement with an all-atom energy function, although computationally expensive, is a powerful method for obtaining accurate structure predictions. Proteins 2007. © 2007 Wiley-Liss, Inc.

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