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Research Article
Classification of protein complexes based on docking difficulty
Article first published online: 24 JUN 2005
DOI: 10.1002/prot.20554
Copyright © 2005 Wiley-Liss, Inc.
Issue
1097-0134/asset/cover.gif?v=1&s=d817e79b67ba6cacf8bdcce1a819c04de300a7e3 "Proteins: Structure, Function, and Bioinformatics")
Proteins: Structure, Function, and Bioinformatics
Special Issue: Second Meeting on the Critical Assessment of PRedicted Interactions
Volume 60, Issue 2, pages 176–180, 1 August 2005
Additional Information
How to Cite
Vajda, S. (2005), Classification of protein complexes based on docking difficulty. Proteins: Structure, Function, and Bioinformatics, 60: 176–180. doi: 10.1002/prot.20554
Publication History
- Issue published online: 24 JUN 2005
- Article first published online: 24 JUN 2005
- Manuscript Accepted: 26 JAN 2005
- Manuscript Received: 18 JAN 2005
Funded by
- National Institutes of Health. Grant Number: GM61867
- Abstract
- Article
- References
- Cited By
Keywords:
- CAPRI docking experiment;
- docking algorithms;
- hydrophobicity;
- interface area;
- conformational change
Abstract
Based on the results of several groups using different docking methods, the key properties that determine the expected success rate in protein–protein docking calculations are measures of conformational change, interface area, and hydrophobicity. A classification of protein complexes in terms of these measures provides a prediction of docking difficulty. This classification is used to study the targets of the CAPRI docking experiment. Results show that targets with a moderate expected difficulty were indeed predicted well by a number of groups, whereas the use of additional a priori information was necessary to obtain good results for some very difficult targets. The analysis indicates that CAPRI and other relatively large-scale docking studies represent very important steps toward understanding the capabilities and limitations of current protein–protein docking methods. Proteins 2005;60:176–180. © 2005 Wiley-Liss, Inc.