Č. Venclovas is also affiliated with Institute of Biotechnology, Vilnius, Lithuania.
1097-0134/asset/PROT_centre.gif?v=1&s=77b56b1f2cdaba74cb3bb149bd9b029cd8803cdb)
Comp. Modelling: Prediction Reports
Comparative modeling in CASP5: Progress is evident, but alignment errors remain a significant hindrance
Article first published online: 15 OCT 2003
DOI: 10.1002/prot.10591
Copyright © 2003 Wiley-Liss, Inc.
Issue
1097-0134/asset/cover.gif?v=1&s=d817e79b67ba6cacf8bdcce1a819c04de300a7e3 "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 380–388, 2003
Additional Information
How to Cite
Venclovas, Č. (2003), Comparative modeling in CASP5: Progress is evident, but alignment errors remain a significant hindrance. Proteins, 53: 380–388. doi: 10.1002/prot.10591
Publication History
- Issue published online: 15 OCT 2003
- Article first published online: 15 OCT 2003
- Manuscript Accepted: 7 APR 2003
- Manuscript Received: 24 FEB 2003
Funded by
- U.S. Department of Energy by the University of California
- Lawrence Livermore National Laboratory. Grant Number: W-7405-ENG-48
- Abstract
- Article
- References
- Cited By
Keywords:
- protein structure prediction;
- sequence-structure alignment;
- 3D model;
- model evaluation;
- distant homology;
- alignment errors
Abstract
Models for 20 comparative modeling targets were submitted for the fifth round of the “blind” test of protein structure prediction methods (CASP5; http://predictioncenter.llnl.gov/casp5). The modeling approach used in CASP5 was similar to that used 2 years ago in CASP4 (Venclovas, Proteins 2001; Suppl 5:47–54). The main features of this approach include use of multiple templates, initial assessment of alignment reliability in a region-specific manner, and structure-based selection of alignment variants in unreliable regions. The CASP5 modeling results presented here show significant improvement in comparison to CASP4, especially in the area of distant homology. The improvements include more effective use of multiple templates and better alignments. However, a number of structurally conserved regions in submitted distant homology models were misaligned. Analysis of these errors indicates that the absolute majority of them occurred in regions deemed unreliable in the course of model building. Most of these error-prone regions can be characterized by their peripheral location and a lack of conserved sequence patterns. For a few of the error-prone regions, all methods evaluated during CASP5 proved ineffective, pointing to the need for more sensitive energy-based methods. Despite these remaining issues, the applicability of comparative modeling continues to expand into more distant evolutionary relationships, providing a means to structurally characterize a significant number of currently available protein sequences. Proteins 2003;53:380–388. © 2003 Wiley-Liss, Inc.