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Updated: Jul 12, 2026
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Modeling Ligands into Maps Derived from Electron Cryomicroscopy
Published on: July 19, 2024
PROCOGNATE: a cognate ligand domain mapping for enzymes
Matthew Bashton1, Irene Nobeli, Janet M Thornton
1EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK. bashton@ebi.ac.uk
Nucleic Acids Research
|August 28, 2007
Summary
PROCOGNATE is a protein ligand database for enzyme structures, now with expanded coverage including Pfam domains. This resource aids researchers by providing cognate ligand information through an interactive website.
Area of Science:
- Biochemistry
- Structural Biology
- Bioinformatics
Background:
- Protein structure databases like CATH, SCOP, and Pfam classify enzyme structures.
- Identifying cognate ligands is crucial for understanding enzyme function and drug discovery.
- Existing resources may lack comprehensive or integrated data on protein-ligand interactions.
Purpose of the Study:
- To provide an overview of the PROCOGNATE database, detailing its generation and features.
- To announce the release of a new website front end for PROCOGNATE.
- To highlight the expanded data coverage of PROCOGNATE, including Pfam domains.
Main Methods:
- Data compilation from CATH, SCOP, and Pfam structural classifications.
- Development of an interactive website for database access and navigation.
- Integration of Pfam domain data to increase dataset coverage.
Main Results:
- The PROCOGNATE database (version 1.3) includes data for 4123 CATH, 4536 SCOP, and 5876 Pfam structures.
- The database covers 377 CATH, 326 SCOP, and 695 Pfam superfamilies/families.
- A new, user-friendly website front end has been implemented.
Conclusions:
- PROCOGNATE serves as a valuable resource for protein cognate ligand information.
- The database's expanded coverage and improved website enhance its utility for researchers.
- PROCOGNATE facilitates the study of enzyme-ligand interactions across multiple structural classifications.
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