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
RefDB: Re-referenced Protein Chemical Shift Database
RefDB website
In case of the BMRB, it is known that a significant portion of depositions use different or non-IUPAC chemical shift reference standards. This lack of uniformity makes it difficult to extract sequence/structure relationships from chemical shifts. Nearly 40% of protein entries deposited in the BioMagResBank appear to have at least one assignment error. In addition, it evident that protein NMR spectroscopists are increasingly adhering to recommended IUPAC (13)C and (15)N chemical shift referencing conventions, however, approximately 20% of newly deposited protein entries in the...
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PACSY, a relational database management system for protein structure and chemical shift analysis
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