PINT: Protein-protein Interactions Thermodynamic Database

Abstract

The first release of Protein-protein Interactions Thermodynamic Database (PINT) contains >1500 data of several thermodynamic parameters along with sequence and structural information, experimental conditions and literature information. Each entry contains numerical data for the free energy change, dissociation constant, association constant, enthalpy change, heat capacity change and so on of the interacting proteins upon binding, which are important for understanding the mechanism of protein-protein interactions. PINT also includes the name and source of the proteins involved in binding, their Protein Information Resource, SWISS-PROT and Protein Data Bank (PDB) codes, secondary structure and solvent accessibility of residues at mutant positions, measuring methods, experimental conditions, such as buffers, ions and additives, and literature information. A WWW interface facilitates users to search data based on various conditions, feasibility to select the terms for output and different sorting options. Further, PINT is cross-linked with other related databases, PIR, SWISS-PROT, PDB and NCBI PUBMED literature database. The database is freely available at http://www.bioinfodatabase.com/pint/index.html.

Figure 1

An example of searching conditions, display and sorting options, and the results of PINT search. (a) Search, display and sorting options: the search is performed for obtaining K_d and ΔG for protein–protein complexes obtained in the temperature range of 15–30° and pH >5. All these search items were selected to display in the output along with PINT code, protein name, peptide name, PDB complex and journal name. The data are sorted with ΔG in descending order. (b) Partial results obtained from PINT under the conditions specified in Figure 1a.