PACSY database, a relational database management system for protein structure and nuclear magnetic resonance chemical shift analysis

摘要

We developed a new relational database management system called PACSY (Protein structure And Chemical Shift NMR spectroscopy) by integrating information from the Protein Data Bank (PDB), the Biological Magnetic Resonance Data Bank (BMRB), and the Structural Classification of Proteins (SCOP) database. PACSY offers valuable information for structural investigations such as three-dimensional coordinates and chemical shifts of atoms along with derived information such as torsion angles, solvent accessible surface areas, and hydrophobicity scales. PACSY consists of six relational table types linked to one another for coherence by key identification numbers. The database can be installed on an RDBMS server such as MySQL and PostgreSQL for advanced search functions by supporting database queries. PACSY enables users to search for combinations of information from different database sources in support of their research. PACSY along with two associated software packages, PACSY Maker for database creation and PACSY Analyzer for database analysis, are available from http://pacsy.nmrfam.wisc.edu.