Skip Navigation



Bioinformatics Advance Access published online on January 31, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm018
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrowOA All Versions of this Article:
23/7/789    most recent
btm018v1
Right arrow Alert me when this article is cited
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 Nicola, G.
Right arrow Articles by Vakser, I. A.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Nicola, G.
Right arrow Articles by Vakser, I. A.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© 2007 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.

A simple shape characteristic of protein-protein recognition

George Nicola 1 and Ilya A. Vakser 2,*

1Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Rd, La Jolla, CA 92037, USA
2Center for Bioinformatics and Department of Molecular Biosciences, The University of Kansas, 2030 Becker Drive, Lawrence, KS 66047, USA

*To whom correspondence should be addressed. Ilya Vakser, E-mail: vakser{at}ku.edu


  Abstract

Motivation: Observation of co-crystallized protein-protein complexes and low-resolution protein-protein docking studies suggest the existence of a binding-related anisotropic shape characteristic of protein-protein complexes.

Results: Our study systematically assessed the global shape of proteins in a non-redundant database of co-crystallized protein-protein complexes by measuring the distance of the surface residues to the protein’s center of mass. The results show that on average the binding site residues are closer to the center of mass than the non-binding surface residues. Thus, the study directly detects an important and simple binding-related characteristic of protein shapes. The results provide an insight into one of the fundamental properties of protein structure and association.

Associate Editor: Anna Tramontano

Received on December 18, 2006; revised on January 15, 2007; accepted on January 17, 2007

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


This article has been cited by other articles:


Home page
 Biophys. JHome page
A. M. Ruvinsky and I. A. Vakser
Chasing Funnels on Protein-Protein Energy Landscapes at Different Resolutions
Biophys. J., September 1, 2008; 95(5): 2150 - 2159.
[Abstract] [Full Text] [PDF]


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.