Skip Navigation


Bioinformatics Advance Access first published online on August 18, 2008
This version published online on August 21, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn432
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrowOA All Versions of this Article:
24/20/2324    most recent
btn432v2
btn432v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Google Scholar
Right arrow Articles by Pulim, V.
Right arrow Articles by Bienkowska, J.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Pulim, V.
Right arrow Articles by Bienkowska, J.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Optimal Contact Map Alignment of Protein-Protein Interfaces

Vinay Pulim 1, Bonnie Berger 1,2,* and Jadwiga Bienkowska 1,3,*

1Computer Science and Artificial Intelligence Laboratory, MIT
2Mathematics Department, MIT
3Biomedical Engineering Department, Boston University

*To whom correspondence should be addressed. Dr. Bonnie Berger, E-mail: bab{at}csail.mit.edu, Dr.Jadwiga Bienkowska, E-mail: jbienkowska{at}gmail.com, jadwiga{at}csail.mit.edu


  Abstract

The long-standing problem of constructing protein structure align-ments is of central importance in computational biology. The main goal is to provide an alignment of residue correspondences, in order to identify homologous residues across chains. A critical next step of this is the alignment of protein complexes and their interfaces. Here we introduce the program CMAPi, a two-dimensional dynamic programming algorithm that, given a pair of protein complexes, optimally aligns the contact maps of their interfaces: it produces polynomial-time near-optimal alignments in the case of multiple complexes. We demonstrate the efficacy of our algorithm on complexes from PPI families listed in the SCOPPI database and from highly divergent cytokine families. In comparison to existing techniques, CMAPi generates more accurate alignments of interacting residues within families of interacting proteins, especially for sequences with low similarity. While previous methods that use an all-atom based representation of the interface have been successful, CMAPi's use of a contact map representation allows it to be more tolerant to conformational changes and thus to align more of the interaction surface. These improved interface alignments should enhance homology modeling and threading methods for predicting PPIs by providing a basis for generating template profiles for sequence-structure alignment.

Supplemental website: http://theory.csail.mit.edu/cmapi

Associate Editor: Prof. Anna Tramontano

Received on April 4, 2008; revised on July 16, 2008; accepted on August 14, 2008

Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?




Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.