Stefan Günther and Patrick May contributed equally to this work.
Docking without docking: ISEARCH—prediction of interactions using known interfaces
Article first published online: 5 SEP 2007
Copyright © 2007 Wiley-Liss, Inc.
Proteins: Structure, Function, and Bioinformatics
Special Issue: Third Meeting on the Critical Assessment of PRedicted Interactions
Volume 69, Issue 4, pages 839–844, December 2007
How to Cite
Günther, S., May, P., Hoppe, A., Frömmel, C. and Preissner, R. (2007), Docking without docking: ISEARCH—prediction of interactions using known interfaces. Proteins, 69: 839–844. doi: 10.1002/prot.21746
- Issue published online: 31 OCT 2007
- Article first published online: 5 SEP 2007
- Manuscript Accepted: 5 JUL 2007
- Manuscript Received: 3 JUN 2007
- prediction of interaction;
The increasing number of solved protein structures provides a solid number of interfaces, if protein–protein interactions, domain–domain contacts, and contacts between biological units are taken into account. An interface library gives us the opportunity to identify surface regions on a target molecule that are similar by local structure and residue composition. If both unbound components of a possible protein complex exhibit structural similarities to a known interface, the unbound structures can be superposed onto the known interfaces. The approach is accompanied by two mathematical problems. Protein surfaces have to be quickly screened by thousands of patches, and similarity has to be evaluated by a suitable scoring scheme. The used algorithm (NeedleHaystack) identifies similar patches within minutes. Structurally related sites are recognized even if only parts of the template patches are structurally related to the interface region. A successful prediction of the protein complex depends on a suitable template of the library. However, the performed tests indicate that interaction sites are identified even if the similarity is very low. The approach complements existing ab initio methods and provides valuable results on standard benchmark sets. Proteins 2007. © 2007 Wiley-Liss, Inc.