Skip Navigation


Bioinformatics Advance Access originally published online on January 19, 2009
Bioinformatics 2009 25(5):615-620; doi:10.1093/bioinformatics/btp035
This Article
Right arrow Full Text
Right arrow Full Text (Print PDF)
Right arrow All Versions of this Article:
25/5/615    most recent
btp035v1
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
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Wallach, I.
Right arrow Articles by Lilien, R.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Wallach, I.
Right arrow Articles by Lilien, R.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

The protein–small-molecule database, a non-redundant structural resource for the analysis of protein-ligand binding

Izhar Wallach 1,* and Ryan Lilien 1,2,*

1Department of Computer Science and 2Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada

*To whom correspondence should be addressed.


  Abstract

Motivation: An enabling resource for drug discovery and protein function prediction is a large, accurate and actively maintained collection of protein/small-molecule complex structures. Models of binding are typically constructed from these structural libraries by generalizing the observed interaction patterns. Consequently, the quality of the model is dependent on the quality of the structural library. An ideal library should be non-biased and comprehensive, contain high-resolution structures and be actively maintained.

Results: We present a new protein/small-molecule database (the PSMDB) that offers a non-redundant set of holo PDB complexes. The database was designed to allow frequent updates through a fully automated process without manual annotation or filtering. Our method of database construction addresses redundancy at both the protein and the small-molecule level. By efficiently handling structures with covalently bound ligands, we allow our database to include a larger number of structures than previous methods. Multiple versions of the database are available at our web site, including structures of split complexes—the proteins without their binding ligands and the non-covalently bound ligands within their native coordinate frame.

Availability: http://compbio.cs.toronto.edu/psmdb

Contact: izharw{at}cs.toronto.edu; lilien{at}cs.toronto.edu

Associate Editor: Burkhard Rost

Received on November 17, 2008; revised on January 8, 2009; accepted on January 13, 2009

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
 BioinformaticsHome page
I. Wallach and R. H. Lilien
Prediction of sub-cavity binding preferences using an adaptive physicochemical structure representation
Bioinformatics, June 15, 2009; 25(12): i296 - i304.
[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.