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

K Abdulla Bava1, M Michael Gromiha, Hatsuho Uedaira

  • 1Department of Biochemical Engineering and Science, Kyushu Institute of Technology (KIT), 680-4 Kawazu, Iizuka, 820-8502, Japan.

Nucleic Acids Research
|December 19, 2003
PubMed
Summary

The ProTherm database now includes 14,500 thermodynamic data points for proteins and mutants, enhancing protein research. This updated thermodynamic database offers improved search capabilities and integrated structural information.

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Bioinformatics

Background:

  • Thermodynamic data is crucial for understanding protein stability and function.
  • Databases integrating thermodynamic, structural, and sequence information are valuable research tools.

Purpose of the Study:

  • To release an updated version of the ProTherm database (Release 4.0).
  • To enhance the ProTherm database with expanded thermodynamic data, structural links, and improved usability.

Main Methods:

  • Compilation of thermodynamic parameters, experimental conditions, and structural information.
  • Integration of data with external protein databases (Protein Data Bank, Protein Information Resource, SWISS-PROT).
  • Development of improved web interface for searching and data display.

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Main Results:

  • ProTherm Release 4.0 contains approximately 14,500 numerical data points, a 450% increase from the first version.
  • Separation of extrapolated Gibbs free energy change from thermal denaturation data.
  • Inclusion of amino acid replacement statistics and homologous structure links for each protein.

Conclusions:

  • The enhanced ProTherm database provides a comprehensive resource for protein thermodynamic and structural data.
  • Improved search functionalities facilitate easier access and analysis of protein information.
  • ProTherm is freely accessible, supporting advancements in protein science.