PROTEIN DATABASES

Exploring proteins without the right databases is like navigating a foreign city with no map. Thankfully, the bioinformatics world offers a vibrant collection of tools, each designed to reveal a different layer of protein identity, structure, function, evolution, and interactions. Whether you're hunting for high-quality curated sequences, predicting 3D structures, tracing domain families, mapping metabolic pathways, or uncovering interaction networks, these databases act as your ultimate scientific toolkit. Together, they turn raw protein data into meaningful biological insight, making research faster, smarter, and far more exciting

Major Protein Databases

	Database	Description	Link
1	UniProtKB/Swiss-Prot	Manually curated, high-quality protein sequence & functional information (domains, PTMs, variants), non‐redundant section of UniProt.	https://www.uniprot.org/
2	UniProtKB/TrEMBL	Automatically annotated supplement of UniProtKB (for sequences not yet in Swiss-Prot).	https://www.uniprot.org/
3	PDB	Protein Data Bank: experimentally determined 3D structures of proteins, nucleic acids, and complexes.	https://www.rcsb.org/
4	GenBank Protein	NCBI repository of protein sequences derived from translations of annotated coding regions in GenBank.	https://www.ncbi.nlm.nih.gov/protein/
5	RefSeq	Curated collection of non-redundant sequences representing reference standard for genomes, transcripts, and proteins.	https://www.ncbi.nlm.nih.gov/refseq/
6	Pfam	Protein families & domains database; provides multiple sequence alignments & hidden Markov models for domain detection.	https://pfam.xfam.org/
7	InterPro	Integration of protein families, domains, functional sites from multiple member databases (including Pfam, PROSITE etc.) and, useful for functional annotation.	https://www.ebi.ac.uk/interpro/
8	PROSITE	Database of protein domains, families and functional sites described by patterns/profiles. Useful for motif scanning.	https://prosite.expasy.org/
9	ModBase	Database of comparative (homology) protein structure models (for proteins without experimental structure).	http://salilab.org/modbase/
10	SCOPe	Structural Classification of Proteins: organizes protein domain structures into hierarchies (class, fold, superfamily, family) for evolutionary context.	https://scop.berkeley.edu/
11	CATH	Another structural classification database (Class, Architecture, Topology, Homology). it is an alternative to SCOPe.	https://www.cathdb.info/
12	STRING	Known & predicted protein-protein interaction (PPI) networks (physical + functional associations) across many organisms.	https://string-db.org/
13	BioGRID	Repository of experimentally determined protein and genetic interactions; valuable for microbial interactome studies.	https://thebiogrid.org/
14	BRENDA	Comprehensive enzyme information system (reaction, kinetics, substrate/product data). It bridges proteins → enzymatic function/pathway.	https://www.brenda-enzymes.org/
15	KEGG Genes/Proteins	Genome‐wide gene/protein sets annotated with pathways, orthology, networks (including bacterial species). Integral to mapping proteins into metabolic pathways.	https://www.genome.jp/kegg/genes.html
16	UniRef	Clusters of UniProt sequences at different identity thresholds (100%, 90%, 50%), helps reduce redundancy and speed searches.	https://www.uniprot.org/uniref/
17	DisProt	Database of intrinsically disordered proteins / regions.	https://disprot.org/
18	Human Protein Atlas	While human-centric, it’s useful as a reference of subcellular localization, expression; analogous bacterial localization databases exist, but this gives idea of protein context.	https://www.proteinatlas.org/