Skip Navigation

This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (PDF) Freely available
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 ISI Web of Science
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
Right arrow Search for citing articles in:
ISI Web of Science (8)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Milik, M.
Right arrow Articles by Olszewski, K. A.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Milik, M.
Right arrow Articles by Olszewski, K. A.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Protein Engineering vol. 16 no. 8 pp. 543-552, 2003
© 2003 Oxford University Press

Common Structural Cliques: a tool for protein structure and function analysis

Mariusz Milik, Sándor Szalma and Krzysztof A. Olszewski1

Accelrys, 9685 Scranton Road, San Diego, CA 92121, USA 1To whom correpsondence should be addressed. e-mail: kato{at}accelrys.com

Proposed is a method for locating functionally relevant atoms in protein structures and a representation of spatial arrangements of these atoms allowing for a flexible description of active sites in proteins. The search method is based on comparison of local structure features of proteins that share a common biochemical function. The method does not depend on overall similarity of structures and sequences of compared proteins or on previous knowledge about functionally relevant residues. The compared protein structures are condensed to a graph representation, with atoms as nodes and distances as edge labels. Protein graphs are then compared to extract all possible Common Structural Cliques. These cliques are merged to create Structural Templates: graphs that describe structural analogies between compared proteins. Structures of serine endopeptidases were compared in pairs using the presented algorithm with different geometrical parameters. Additionally, a Structural Template was extracted from the structures of aminotransferases, two different proteins that catalyze the same type of chemical reaction. The results presented show that the method works efficiently even in the case of large protein systems and allows for extraction of common structural features from proteins catalyzing a particular chemical reaction, but that evolved from different ancestors by convergent evolution.

Received March 9, 2003; revised June 6, 2003; accepted June 24, 2003.


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
 Nucleic Acids ResHome page
K. Goyal, D. Mohanty, and S. C. Mande
PAR-3D: a server to predict protein active site residues
Nucleic Acids Res., July 13, 2007; 35(suppl_2): W503 - W505.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
A. Sacan, O. Ozturk, H. Ferhatosmanoglu, and Y. Wang
LFM-Pro: a tool for detecting significant local structural sites in proteins
Bioinformatics, March 15, 2007; 23(6): 709 - 716.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
X. Yuan and C. Bystroff
Non-sequential structure-based alignments reveal topology-independent core packing arrangements in proteins
Bioinformatics, April 1, 2005; 21(7): 1010 - 1019.
[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.