Predictions from Automatic Servers

CAFASP3 in the spotlight of EVA

  1. Volker A. Eyrich1,
  2. Dariusz Przybylski1,2,4,
  3. Ingrid Y.Y. Koh1,2,
  4. Osvaldo Grana5,
  5. Florencio Pazos6,
  6. Alfonso Valencia5,
  7. Burkhard Rost1,2,3,*

Article first published online: 15 OCT 2003

DOI: 10.1002/prot.10534

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 548–560, 2003

Additional Information

How to Cite

Eyrich, V. A., Przybylski, D., Koh, I. Y.Y., Grana, O., Pazos, F., Valencia, A. and Rost, B. (2003), CAFASP3 in the spotlight of EVA. Proteins, 53: 548–560. doi: 10.1002/prot.10534

Author Information

  1. 1

    CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York

  2. 2

    Columbia University Center for Computational Biology and Bioinformatics (C2B2), New York, New York

  3. 3

    North East Structural Genomics Consortium (NESG), Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York

  4. 4

    Department of Physics, Columbia University, New York, New York

  5. 5

    Protein Design Group, Centro Nacional de Biotecnologia (CNB-CSIC), Cantoblanco, Madrid, Spain

  6. 6

    ALMA Bioinformatica, Contoblanco, Madrid, Spain

*CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, 630 West 168th St., BB 217, New York, NY 10032

Publication History

  1. Issue published online: 15 OCT 2003
  2. Article first published online: 15 OCT 2003
  3. Manuscript Accepted: 19 MAY 2003
  4. Manuscript Received: 28 FEB 2003

Funded by

  • Spanish Ministry of Science and Technology. Grant Number: BIO2000-1358-CO2-01
  • TEMBLOR. Grant Number: CSIC:LIFE/001/0957 UE:QLRT-2001-00015
  • SANITAS. Grant Number: CSIC:LIFE/992/0553 UE:QLK3-CT-2000-00079
  • RAS. Grant Number: CSIC:LIFE/991/0219 UE:QLK3-CT-1999-00875
  • National Institutes of Health. Grant Numbers: 5-P20-LM7276, RO1-GM63029-01

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Keywords:

  • protein structure prediction;
  • evaluation;
  • secondary structure;
  • inter-residue distances;
  • contact maps;
  • threading;
  • fold recognition;
  • automatic servers

Abstract

We have analysed fold recognition, secondary structure and contact prediction servers from CAFASP3. This assessment was carried out in the framework of the fully automated, web-based evaluation server EVA. Detailed results are available at http://cubic.bioc.columbia.edu/eva/cafasp3/. We observed that the sequence-unique targets from CAFASP3/CASP5 were not fully representative for evaluating performance. For all three categories, we showed how careless ranking might be misleading. We compared methods from all categories to experts in secondary structure and contact prediction and homology modellers to fold recognisers. While the secondary structure experts clearly outperformed all others, the contact experts appeared to outperform only novel fold methods. Automatic evaluation servers are good at getting statistics right and at using these to discard misleading ranking schemes. We challenge that to let machines rule where they are best might be the best way for the community to enjoy the tremendous benefit of CASP as a unique opportunity for brainstorming. Proteins 2003;53:548–560. © 2003 Wiley-Liss, Inc.

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