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

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 (approximately 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.

ProTherm, version 4.0: thermodynamic database for proteins and mutants.

Release 4.0 of ProTherm, thermodynamic database for proteins and mutants, contains approximately 14,500 numerical data (approximately 450% of the first version) of several thermodynamic parameters along with experimental methods and conditions, and structural, functional and literature information. The sequence and structural information of proteins is connected with thermodynamic data through links between entries in Protein Data Bank, Protein Information Resource and SWISS-PROT and the data in ProTherm. We have separated the Gibbs free energy change obtained at extrapolated temperature from the data on denaturation temperature measured by the thermal denaturation method. We have added the statistics of amino acid replacements and links to homologous structures to each protein. Further, we have improved the search and display options to enhance search capability through the web interface. ProTherm is freely available at http://gibk26. bse.kyutech.ac.jp/jouhou/Protherm/protherm.html.