Introduction
Protein databases are specialized biological repositories that store protein sequences, three-dimensional structures, functional annotations, protein families, domains, and evolutionary relationships. These databases are essential resources in bioinformatics, proteomics, molecular biology, structural biology, and drug discovery. Researchers use protein databases to identify proteins, analyze their functions, study protein interactions, predict structures, and understand evolutionary relationships.
Major protein databases include UniProt, Protein Data Bank (PDB), InterPro, and protein classification databases such as SCOP and CATH.
UniProt (Swiss-Prot / TrEMBL)
UniProt (Universal Protein Resource) is the world’s leading database for protein sequence and functional information. It provides comprehensive protein data collected from multiple sources and serves as a central resource for protein annotation and biological research.
UniProt consists of two major sections:
- Swiss-Prot – A manually reviewed and curated database containing high-quality protein sequences with experimentally validated functional annotations.
- TrEMBL – An automatically annotated database containing computationally analyzed protein sequences awaiting manual review.
Researchers use UniProt for protein identification, functional annotation, sequence analysis, protein localization, enzyme information, and protein interaction studies.
Website: https://www.uniprot.org/
Protein Data Bank (PDB)
The Protein Data Bank (PDB) is the world’s primary repository of three-dimensional structures of proteins, nucleic acids, and complex biomolecules. The database contains experimentally determined structures generated using techniques such as:
- X-ray crystallography
- Nuclear Magnetic Resonance (NMR) spectroscopy
- Cryo-Electron Microscopy (Cryo-EM)
PDB plays a crucial role in structural biology, drug discovery, molecular modeling, protein engineering, and understanding biomolecular interactions.
Website: https://www.rcsb.org/
InterPro
InterPro is an integrated database that classifies proteins into families and predicts the presence of protein domains, functional sites, and important conserved regions. It combines protein signatures from several member databases into a single unified resource.
Researchers use InterPro to:
- Identify protein families
- Detect conserved protein domains
- Predict protein function
- Analyze functional sites
- Study evolutionary relationships
InterPro is widely used in genome annotation and functional genomics research.
Website: https://www.ebi.ac.uk/interpro
SCOP / CATH
SCOP (Structural Classification of Proteins)
SCOP is a manually curated database that classifies proteins according to their three-dimensional structures and evolutionary relationships. It organizes proteins into a hierarchical system based on structural similarities, making it valuable for studying protein evolution and structural biology.
Website: https://scop.mrc-lmb.cam.ac.uk/
CATH (Class, Architecture, Topology, Homologous Superfamily)
CATH is a comprehensive protein structure classification database that uses automated computational methods, supported by expert manual validation, to organize proteins into hierarchical structural categories. It assists researchers in understanding protein evolution, function, and structural relationships.
Website: https://www.cathdb.info/