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Updated: May 19, 2026
09:51
Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
PACSY, a relational database management system for protein structure and chemical shift analysis
Woonghee Lee1, Wookyung Yu, Suhkmann Kim
1National Magnetic Resonance Facility at Madison, and Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706, USA. whlee@nmrfam.wisc.edu
Journal of Biomolecular NMR
|August 21, 2012
Summary
PACSY is a relational database integrating protein structure and chemical shift data. It aids researchers by enabling complex queries across multiple biological databases.
Area of Science:
- Biochemistry
- Structural Biology
- Bioinformatics
Background:
- NMR spectroscopy is crucial for determining protein structure and dynamics.
- Integrating diverse biological data sources enhances research capabilities.
- Existing databases may lack comprehensive integration of chemical shift and structural data.
Purpose of the Study:
- To introduce PACSY (Protein structure And Chemical Shift NMR spectroscopY), a novel relational database management system.
- To facilitate integrated data retrieval for protein structure and NMR chemical shift information.
- To support advanced research queries by combining data from multiple sources.
Main Methods:
- Developed a relational database system (PACSY) with six linked table types.
- Integrated data from the Protein Data Bank, Biological Magnetic Resonance Data Bank, and Structural Classification of Proteins.
- Implemented advanced search functions using RDBMS servers (MySQL, PostgreSQL).
- Created PACSY Maker for database creation and PACSY Analyzer for analysis.
Main Results:
- PACSY successfully integrates 3D coordinates, chemical shifts, torsion angles, solvent accessible surface areas, and hydrophobicity scales.
- The system supports complex, cross-database queries.
- Software for database creation and analysis is available.
Conclusions:
- PACSY provides a unified platform for accessing and analyzing integrated protein structure and chemical shift data.
- The database enhances research efficiency by simplifying data retrieval.
- PACSY is a valuable resource for structural biologists and biochemists utilizing NMR data.
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