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Default PACSY, a relational database management system for protein structure and chemical shift analysis

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


Abstract PACSY (Protein structure And Chemical Shift NMR spectroscopY) is a relational database management system that integrates information from the Protein Data Bank, the Biological Magnetic Resonance Data Bank, and the Structural Classification of Proteins database. PACSY provides 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. Database queries are enabled by advanced search functions supported by an RDBMS server such as MySQL or PostgreSQL. PACSY enables users to search for combinations of information from different database sources in support of their research. Two software packages, PACSY Maker for database creation and PACSY Analyzer for database analysis, are available from http://pacsy.nmrfam.wisc.edu.
  • Content Type Journal Article
  • Category Article
  • Pages 1-11
  • DOI 10.1007/s10858-012-9660-3
  • Authors
    • Woonghee Lee, National Magnetic Resonance Facility at Madison, and Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706, USA
    • Wookyung Yu, Department of Physics, Center for Proteome Biophysics, Pusan National University, Busan, 609-735 Korea
    • Suhkmann Kim, Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan, 609-735 Korea
    • Iksoo Chang, Department of Physics, Center for Proteome Biophysics, Pusan National University, Busan, 609-735 Korea
    • Weontae Lee, Structural Biochemistry and Molecular Biophysics Laboratory, Department of Biochemistry, Yonsei University, Seoul, 120-749 Korea
    • John L. Markley, National Magnetic Resonance Facility at Madison, and Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706, USA

Source: Journal of Biomolecular NMR
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