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J Biomol NMR. 2012 Oct;54(2):169-79. Epub 2012 Aug 19.

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

Author information

1
National Magnetic Resonance Facility at Madison, and Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706, USA. whlee@nmrfam.wisc.edu

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.

PMID:
22903636
PMCID:
PMC3542970
DOI:
10.1007/s10858-012-9660-3
[Indexed for MEDLINE]
Free PMC Article
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