Literature DB >> 22903636

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

Woonghee Lee1, Wookyung Yu, Suhkmann Kim, Iksoo Chang, Weontae Lee, John L Markley.   

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.

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Year:  2012        PMID： 22903636      PMCID： PMC3542970          DOI： 10.1007/s10858-012-9660-3

Source DB:  PubMed          Journal:  J Biomol NMR        ISSN： 0925-2738            Impact factor:   2.835


  39 in total

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5.  Recommendations for the presentation of NMR structures of proteins and nucleic acids. IUPAC-IUBMB-IUPAB Inter-Union Task Group on the Standardization of Data Bases of Protein and Nucleic Acid Structures Determined by NMR Spectroscopy.

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  16 in total

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8.  NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy.

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9.  pH-induced conformational change of IscU at low pH correlates with protonation/deprotonation of two conserved histidine residues.

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