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A Web Tool for Generating High Quality Machine-readable Biological Pathways
Published on: February 8, 2017
SKPDB: a structural database of shikimate pathway enzymes
Helen A Arcuri1, Geraldo Fd Zafalon, Evandro A Marucci
1CEIS/Departamento de Biologia, Instituto de Biociências, UNESP, Rio Claro, São Paulo, Brasil.
BMC Bioinformatics
|January 9, 2010
Summary
The ShiKimate Pathway DataBase (SKPDB) offers extensive enzyme data for microbial metabolic pathways. This resource aids in developing targeted drugs by providing structural and functional information on essential bacterial enzymes not found in humans.
Area of Science:
- Biochemistry
- Structural Biology
- Bioinformatics
Background:
- Enzyme characterization is crucial for structure-based drug design.
- Shikimate pathway enzymes are essential in bacteria but absent in humans, making them ideal drug targets.
- Understanding microbial metabolic pathways aids in selective drug development.
Purpose of the Study:
- To present the ShiKimate Pathway DataBase (SKPDB) as a resource for studying shikimate pathway enzymes.
- To provide a comprehensive collection of structural and functional data for drug design initiatives.
- To facilitate research on microbial enzymes for therapeutic applications.
Main Methods:
- Developed and maintain the ShiKimate Pathway DataBase (SKPDB).
- Integrated sequence, structural, and functional data for shikimate pathway enzymes.
- Made enzyme data, including atomic coordinates and quality scores, downloadable.
- Enabled visualization of modeled structures using Jmol.
Main Results:
- The SKPDB currently houses 8902 enzymes from the shikimate pathway.
- The database provides detailed information on enzyme sequences, references, and studies.
- All primary sequence, atomic coordinates, and quality scores are available for download.
Conclusions:
- SKPDB offers a substantial collection of structural models for docking simulations and virtual screening.
- The database is a valuable tool for structure-based drug design targeting microbial enzymes.
- SKPDB is freely accessible online for research purposes.
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