Predictions from Automatic Servers

LiveBench-6: Large-scale automated evaluation of protein structure prediction servers

  1. Leszek Rychlewski1,*,
  2. Daniel Fischer2,
  3. Arne Elofsson3

Article first published online: 15 OCT 2003

DOI: 10.1002/prot.10535

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 542–547, 2003

Additional Information

How to Cite

Rychlewski, L., Fischer, D. and Elofsson, A. (2003), LiveBench-6: Large-scale automated evaluation of protein structure prediction servers. Proteins, 53: 542–547. doi: 10.1002/prot.10535

Author Information

  1. 1

    Bioinformatics Laboratory, BioInfoBank Institute, Poznan, Poland

  2. 2

    Bioinformatics, Department of Computer Science, Ben Gurion University, Beer-Sheva, Israel

  3. 3

    Stockholm Bioinformatics Center, Stockholm University, Stockholm, Sweden

*Bioinformatics Laboratory, BioInfoBank Institute, ul. Limanowskiego 24A, 60-744 Poznan, Poland

Publication History

  1. Issue published online: 15 OCT 2003
  2. Article first published online: 15 OCT 2003
  3. Manuscript Accepted: 15 MAY 2003
  4. Manuscript Received: 17 FEB 2003

Funded by

  • Swedish Strategic Research Foundation
  • Carl Trygger Foundation
  • Swedish National Research Council

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Keywords:

  • protein structure prediction;
  • consensus fold recognition;
  • CAFASP;
  • Meta-Server;
  • ToolShop;
  • LiveBench

Abstract

The aim of the LiveBench experiment is to provide a continuous evaluation of structure prediction servers in order to inform potential users about the current state-of-the-art structure prediction tools and in order to help the developers to analyze and improve the services. This round of the experiment was conducted in parallel to the blind CAFASP-3 evaluation experiment. The data collected almost simultaneously enables the comparison of servers on two different benchmark sets. The number of servers has doubled from the last evaluated LiveBench-4 experiment completed in April 2002, just before the beginning of CAFASP-3. This can be partially attributed to the rapid development in the area of meta-predictors (consensus servers). The current results confirm the high sensitivity and specificity of the meta-predictors. Nevertheless, the comparison between the autonomous (not meta) servers participating in the last CAFASP-2 and LiveBench-2 experiment and the current set of autonomous servers demonstrates that progress has been made also in sequence structure fitting functions. In addition to the growing number of participants, the current experiment marks the introduction of new evaluation procedures, which are aimed to correlate better with functional characteristics of models. Proteins 2003;53:542–547. © 2003 Wiley-Liss, Inc.

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