1097-0134/asset/PROT_centre.gif?v=1&s=77b56b1f2cdaba74cb3bb149bd9b029cd8803cdb)
Numerical Evaluation Method
Automated large scale evaluation of protein structure predictions
Article first published online: 8 NOV 1999
DOI: 10.1002/(SICI)1097-0134(1999)37:3+<7::AID-PROT3>3.0.CO;2-V
Copyright © 1999 Wiley-Liss, Inc.
Issue
1097-0134/asset/cover.gif?v=1&s=d817e79b67ba6cacf8bdcce1a819c04de300a7e3 "Proteins: Structure, Function, and Bioinformatics")
Proteins: Structure, Function, and Bioinformatics
Supplement: Third Meeting on the Critical Assessment of Techniques for Protein Structure Prediction
Volume 37, Issue Supplement 3, pages 7–14, 1999
Additional Information
How to Cite
Lackner, P., Koppensteiner, W. A., Domingues, F. S. and Sippl, M. J. (1999), Automated large scale evaluation of protein structure predictions. Proteins, 37: 7–14. doi: 10.1002/(SICI)1097-0134(1999)37:3+<7::AID-PROT3>3.0.CO;2-V
Publication History
- Issue published online: 8 NOV 1999
- Article first published online: 8 NOV 1999
- Manuscript Accepted: 7 JUN 1999
- Manuscript Received: 12 MAR 1999
Funded by
- Fonds zur Förderung der Wissenschaflichen Forschung. Grant Number: P11601-GEN and P11205-MOB
- Fundação para a Ciência e a Tecnologia. Grant Number: PRAXIS XX1/BD/4528/94
- Abstract
- Article
- References
- Cited By
Keywords:
- CASP;
- structure comparison;
- structure similarity;
- alternative alignments
Abstract
Evaluation and assessment are critical issues in CASP experiments. Automated procedures are necessary to compare a large number of predictions with the target folds. The evaluation has to reveal the maximum extent of similarity between predictions and targets, it should be applicable across prediction categories, and it should be transparent and accessible to a wide community. Here we present an automated evaluation scheme which is an attempt to meet these requirements. In the implementation and execution of this scheme we had to solve or circumvent problems of convergence, where algorithms fail to find optimum solutions, problems of ambiguity where no unique optimum solution exists, and problems in ranking and interpretation. Key features of this implementation are (1) the root mean square deviation of structure superimposition is kept close to a constant value throughout the evaluation and (2) all structural matches found between two folds are taken into account. We discuss these points in detail and describe the numerical criteria used in the CASP3 evaluation. Proteins Suppl 1999;3:7–14. © 1999 Wiley-Liss, Inc.