Recent Developments in ProTherm: Thermodynamic Database for Proteins and Mutants

Due to the rapid progress in genome analysis, complete genome sequences of many organisms become available. Now proteins are the next target for intensive study, as evidenced by the emerging fields such as structural genomics and proteome analysis. In order to elucidate molecular function of proteins, we need to have knowledge of their amino acid sequence and structure. The sequence and structural information, however, is not enough to infer the protein function, because protein is a microscopic entity and its behavior obeys the law of thermodynamics. Thus, the information of thermodynamic quantities of proteins and their interactions is as fundamental as sequence and structural information. Although the databases for sequence and structure are well established and available, databases for thermodynamic quantities on protein stability and interactions are few. Thermodynamic data for proteins are essential not only for understanding the mechanism of protein folding and stability, but also for designing stable mutants. The compilation of thermodynamic data along with the sequence, structural, functional and literature information would be a valuable resource for such studies [2, 4]. Thus, we have designed an electronically accessible database, ProTherm [3], including several thermodynamic parameters, along with sequence and structural information, experimental methods and conditions, and literature information. Further, we have provided a WWW interface to facilitate searching the database, sorting and visualizing the results. Currently ProTherm contains about 12,000 entries.