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Nucleic Acids Research Advance Access published online on October 4, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm784
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© 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.

Database Issue

DB-PABP: a database of polyanion-binding proteins

Jianwen Fang1,2,*, Yinghua Dong1, Nazila Salamat-Miller3 and C. Russell Middaugh4

1Bioinformatics Core Facility, 2Information and Telecommunication Technology Center, University of Kansas, Lawrence, KS 66047, 3Shire Human Genetic Therapeutics, Cambridge, MA 02139 and 4Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS 66047, USA

*To whom correspondence should be addressed. Tel: +1 785 864 3349; Fax: +1 785 864 5738; Email: jwfang{at}ku.edu

Received August 10, 2007. Revised September 12, 2007. Accepted September 17, 2007.

The interactions between polyanions (PAs) and polyanion-binding proteins (PABPs) have been found to play significant roles in many essential biological processes including intracellular organization, transport and protein folding. Furthermore, many neurodegenerative disease-related proteins are PABPs. Thus, a better understanding of PA/PABP interactions may not only enhance our understandings of biological systems but also provide new clues to these deadly diseases. The literature in this field is widely scattered, suggesting the need for a comprehensive and searchable database of PABPs. The DB-PABP is a comprehensive, manually curated and searchable database of experimentally characterized PABPs. It is freely available and can be accessed online at http://pabp.bcf.ku.edu/DB_PABP/. The DB-PABP was implemented as a MySQL relational database. An interactive web interface was created using Java Server Pages (JSP). The search page of the database is organized into a main search form and a section for utilities. The main search form enables custom searches via four menus: protein names, polyanion names, the source species of the proteins and the methods used to discover the interactions. Available utilities include a commonality matrix, a function of listing PABPs by the number of interacting polyanions and a string search for author surnames. The DB-PABP is maintained at the University of Kansas. We encourage users to provide feedback and submit new data and references.


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