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Bioinformatics Advance Access published online on August 25, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm395
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© The Author (2007). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

MeTaDoR: A comprehensive resource for membrane targeting domains and their host proteins

Nitin Bhardwaj 1, Robert V. Stahelin 2, Guijun Zhao 1, Wonhwa Cho 3 and Hui Lu 1,*

1Bioinformatics Program, 1Department of Bioengineering, and 3Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, USA. 2Department of Biochemistry and Molecular Biology, Indiana University School of Medicine-South Bend and the Department of Chemistry and Biochemistry and the Walther Center for Cancer Research, University of Notre Dame South Bend, IN 46617, USA.

*To whom correspondence should be addressed. Prof. Hui Lu, E-mail: huilu{at}uic.edu


  Abstract

Motivation: Protein-lipid interactions play a central role in cellular signaling and membrane trafficking and at the core of these interactions are domains specialized in lipid binding and membrane targeting. Considering the importance of these domains, we have created MeTaDoR, a comprehensive resource dedicated to membrane targeting domains (MTDs).

Results: MeTaDoR begins with a brief introduction about all the important MTDs including their subcellular localization and structural features. Sequences of all known MTDs are then provided in two formats: standard Prosite format and a parsed tab-delimited format that provides a manually curated classification into binding or non-binding. Structures of all MTDs and host proteins known so far are provided with links to PDB and Pfam databases. Membrane-binding orientation of these proteins, whether experimentally determined or proposed, is also provided with links to the appropriate literature. To facilitate molecular dynamics studies of these proteins, the force-field parameters for many non-standard lipids that commonly interact with these proteins are also provided. Finally, an online server for predicting membrane-binding proteins and a search function with various search-fields are included. The resource is publicly available and will be updated on a regular basis.

Availability: http://proteomics.bioengr.uic.edu/metador

Contact: huilu{at}uic.edu

Associate Editor: Prof. Alfonso Valencia

Received on April 15, 2007; revised on July 6, 2007; accepted on July 30, 2007

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