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

Woonghee Lee, Wookyung Yu, Suhkmann Kim, Iksoo Chang, Weontae Lee, John L. Markley

Research output: Contribution to journalArticle

18 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)169-179
Number of pages11
JournalJournal of Biomolecular NMR
Volume54
Issue number2
DOIs
Publication statusPublished - 2012 Oct 1

Fingerprint

Database Management Systems
Chemical shift
Databases
Proteins
Magnetic Resonance Spectroscopy
Protein Databases
Magnetic resonance
Hydrophobicity
Hydrophobic and Hydrophilic Interactions
Software packages
Torsional stress
Nuclear magnetic resonance spectroscopy
Servers
Software
Atoms
Research

All Science Journal Classification (ASJC) codes

  • Biochemistry
  • Spectroscopy

Cite this

Lee, Woonghee ; Yu, Wookyung ; Kim, Suhkmann ; Chang, Iksoo ; Lee, Weontae ; Markley, John L. / PACSY, a relational database management system for protein structure and chemical shift analysis. In: Journal of Biomolecular NMR. 2012 ; Vol. 54, No. 2. pp. 169-179.
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PACSY, a relational database management system for protein structure and chemical shift analysis. / Lee, Woonghee; Yu, Wookyung; Kim, Suhkmann; Chang, Iksoo; Lee, Weontae; Markley, John L.

In: Journal of Biomolecular NMR, Vol. 54, No. 2, 01.10.2012, p. 169-179.

Research output: Contribution to journalArticle

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