Domain: Prediction

Assessment of predictions submitted for the CASP7 domain prediction category

  1. Michael Tress1,*,
  2. Jianlin Cheng2,
  3. Pierre Baldi3,
  4. Keehyoung Joo4,
  5. Jinwoo Lee4,
  6. Joo-Hyun Seo4,5,
  7. Jooyoung Lee4,
  8. David Baker6,7,
  9. Dylan Chivian8,
  10. David Kim6,
  11. Iakes Ezkurdia1

Article first published online: 6 AUG 2007

DOI: 10.1002/prot.21675

Issue

Proteins: Structure, Function, and Bioinformatics

Proteins: Structure, Function, and Bioinformatics

Supplement: Proteins

Volume 69, Issue Supplement S8, pages 137–151, 2007

Additional Information

How to Cite

Tress, M., Cheng, J., Baldi, P., Joo, K., Lee, J., Seo, J.-H., Lee, J., Baker, D., Chivian, D., Kim, D. and Ezkurdia, I. (2007), Assessment of predictions submitted for the CASP7 domain prediction category. Proteins: Structure, Function, and Bioinformatics, 69: 137–151. doi: 10.1002/prot.21675

Author Information

  1. 1

    Structural and Biological Computation Programme, Spanish National Cancer Research Centre, Madrid, Spain

  2. 2

    School of Electrical Engineering and Computer Science, University of Central Florida, Orlando, Florida

  3. 3

    Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California, Irvine, California

  4. 4

    School of Computational Sciences, Korea Institute for Advanced Study, Seoul 130-722, Korea

  5. 5

    School of Chemical and Biological Engineering, Seoul National University, Seoul 151-742, Korea

  6. 6

    Department of Biochemistry, University of Washington, Seattle, Washington

  7. 7

    Howard Hughes Medical Institute, Seattle, Washington

  8. 8

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

*Structural and Biological Computation Programme, Spanish National Cancer Research Centre, c./ Melchor Fernandez Almagro, Madrid, Spain

Publication History

  1. Issue published online: 30 OCT 2007
  2. Article first published online: 6 AUG 2007
  3. Manuscript Accepted: 5 JUN 2007
  4. Manuscript Revised: 21 MAY 2007
  5. Manuscript Received: 1 MAR 2007

Funded by

  • BioSapiens Network of Excellence. Grant Number: LSHC-CT-2003-505265

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Keywords:

  • domain boundaries;
  • domain overlap;
  • evaluation;
  • ab initio domain prediction;
  • template-based domain prediction;
  • proteins

Abstract

This paper details the assessment process and evaluation results for the Critical Assessment of Protein Structure Prediction (CASP7) domain prediction category. Domain predictions were assessed using the Normalized Domain Overlap score introduced in CASP6 and the accuracy of prediction of domain break points. The results of the analysis clearly demonstrate that the best methods are able to make consistently reliable predictions when the target has a structural template, although they are less good when the domain break occurs in a region not covered by a template. The conditions of the experiment meant that it was impossible to draw any conclusions about domain prediction for free modeling targets and it was also difficult to draw many distinctions between the best groups. Two thirds of the targets submitted were single domains and hence regarded as easy to predict. Even those targets defined as having multiple domains always had at least one domain with a similar template structure. Proteins 2007. © 2007 Wiley-Liss, Inc.

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