InterPro is a database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to unknown protein sequences.

The mission of UniProt is to provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information.

UniProt (Universal Protein Resource) is the world's most comprehensive catalogue of information on proteins. It is a central repository of protein sequence and function created by joining the information contained in UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and PIR.

Online text-based search and retrieval system used at NCBI for finding proteins by keywords, id number, database number, etc. The protein entries in the Entrez search and retrieval system have been compiled from a variety of sources, including SwissProt, PIR, PRF, PDB, and translations from annotated coding regions in GenBank and RefSeq.

BioThesaurus is a web-based system designed to map a comprehensive collection of protein and gene names to UniProt Knowledgebase (UniProtKB) protein entries.

Multiple search entries on Uniprto/SwissProt/TrEMBL

SIRW is a web interface to SIR (Simple Indexing and Retrieval System). SIR provides the ability to simultaneously search a protein database with a sequence motif pattern and keywords, e.g. useful for restricting a pattern search to a database subset.

Information Hyperlinked over Proteins. A protein data harvester.

Database of cognate ligands for the domains of enzyme structures in CATH, SCOP and Pfam.

Several search tools based on multiple criterias such as physical or chemical properties, sequence, peptides, or text strings.

Biozon is a unified biological resource on DNA sequences, proteins, complexes and cellular pathways.

Yeast resource center public data repository protein database

The Protein Ligand Database is a resource containing biomolecular data, including binding energies, Tanimoto ligand similarity scores and protein sequence similarities of protein-ligand complexes.

Xpro is a relational database that contains all the eukaryotic protein-encoding DNA sequences in GenBank. It provides detailed and comprehensive features about both the intron containing and the intron-less genes.

The HUGE protein database are expected to cover various sets of large human proteins of hitherto unidentified functions.

Database for Localization, Interaction, Functional assays and Expression of Proteins