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PRENRL_3D: a computer program for an automatic creation of NRL_3D, protein sequence-structure database, from the
M Kusunoki1, D G George, K Namboodiri
1National Biomedical Research Foundation, Georgetown University Medical Center, Washington, DC 20007.
Protein Sequences & Data Analysis
|December 1, 1991
Summary
A new program, PRENRL_3D, automates the extraction of protein sequence-structure data from the Protein Data Bank (PDB). This enhances the NRL_3D database, improving protein structure analysis efficiency.
Area of Science:
- Bioinformatics
- Structural Biology
- Computational Biology
Background:
- The NRL_3D database provides access to protein sequence-structure information.
- Manual updates of NRL_3D from the Protein Data Bank (PDB) are inefficient.
- Protein sequence analysis requires accurate and accessible structural data.
Purpose of the Study:
- To develop an automated method for updating the NRL_3D database.
- To improve the efficiency of extracting protein 3D coordinates from the PDB.
- To facilitate customized database creation based on specific PDB entry criteria.
Main Methods:
- Developed a C computer language program, PRENRL_3D, for automated data extraction.
- Ensured program portability across different computer systems.
- Implemented modular design with generalized procedures for PDB data manipulation.
Main Results:
- PRENRL_3D successfully automates the extraction of NRL_3D from the PDB.
- The program allows for customized NRL_3D database creation based on resolution and R-value.
- Automated extraction significantly reduces the time and effort required for database updates.
Conclusions:
- PRENRL_3D offers an efficient and portable solution for maintaining the NRL_3D database.
- Automated data extraction streamlines protein structure analysis workflows.
- The developed program enhances accessibility to crucial protein structural information for researchers.