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 journalArticlepeer-review

20 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

Bibliographical note

Funding Information:
Acknowledgments This work was supported by NIH grants from the National Center for Research Resources (5P41RR002301-27 and RR02301-26S1) and the National Institute for General Medical Sciences (8 P41 GM103399-27) that support the National Magnetic Resonance Facility at Madison (NMRFAM). W.Y. and I.C. were supported by the Creative Research Initiative (No. 2011-0000041) to Center for Proteome Biophysics from National Research Foundation/Ministry of Education, Science and Technology, Korea. We thank Dimitri Maziuk for technical support of the NMRFAM computer network. All the work performed in this paper is based on the versions of PDB and BMRB available on February 7, 2012 and on the 1.75 version of the SCOP database.

All Science Journal Classification (ASJC) codes

  • Biochemistry
  • Spectroscopy

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