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Nucleic Acids Research 2006 34(Database Issue):D204-D206; doi:10.1093/nar/gkj103
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Nucleic Acids Research, 2006, Vol. 34, Database issue D204-D206
© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Article

ProTherm and ProNIT: thermodynamic databases for proteins and protein–nucleic acid interactions

M. D. Shaji Kumar1, K. Abdulla Bava1, M. Michael Gromiha2, Ponraj Prabakaran3, Koji Kitajima1, Hatsuho Uedaira4 and Akinori Sarai*

Department of Bioscience and Bioinformatics, Kyushu Institute of Technology (KIT) 680-4 Kawazu Iizuka, 820-8502 Japan 1Advanced Technology Institute, Inc. (ATI) 2-3-13-103 Tate, Shiki, Saitama 353-0006, Japan 2Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST) AIST Tokyo Waterfront Bio-IT Research Building, 2-42 Aomi, Koto-ku, Tokyo 135-0064, Japan 3Laboratory of Experimental and Computational Biology, NCI, NIH Frederick, MD 21702, USA 4Tsukuba Materials Information Laboratory 3-23-4, Ninomiya, Tsukuba, 305-0051 Japan

*To whom correspondence should be addressed. Tel: +81 948 29 7811; Fax: +81 948 29 7841; Email: sarai{at}bse.kyutech.ac.jp

Received September 15, 2005. Revised October 14, 2005. Accepted October 14, 2005.

ProTherm and ProNIT are two thermodynamic databases that contain experimentally determined thermodynamic parameters of protein stability and protein–nucleic acid interactions, respectively. The current versions of both the databases have considerably increased the total number of entries and enhanced search interface with added new fields, improved search, display and sorting options. As on September 2005, ProTherm release 5.0 contains 17 113 entries from 771 proteins, retrieved from 1497 scientific articles (~20% increase in data from the previous version). ProNIT release 2.0 contains 4900 entries from 273 research articles, representing 158 proteins. Both databases can be queried using WWW interfaces. Both quick search and advanced search are provided on this web page to facilitate easy retrieval and display of the data from these databases. ProTherm is freely available online at http://gibk26.bse.kyutech.ac.jp/jouhou/Protherm/protherm.html and ProNIT at http://gibk26.bse.kyutech.ac.jp/jouhou/pronit/pronit.html.


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