Proteinnaming

Proteinnaming is the practice of assigning and standardizing names for protein molecules in databases and literature. Names reflect gene origin, function, or structural features, and aim to be unambiguous across studies. Because many proteins have historic names, multiple naming traditions coexist, sometimes causing confusion between gene symbols and mature proteins.

Common conventions include deriving the protein name from the encoding gene symbol (for example, the INS gene producing insulin), or using a descriptive functional name. In humans, approved symbols come from the HGNC; UniProt provides a recommended protein name for each entry, often with the gene symbol and short description. Enzyme names may follow IUBMB EC numbers.

Proteins can exist as multiple proteoforms due to alternative splicing and post-translational modifications. These forms may have distinct names or isoform identifiers; UniProt and other databases track canonical sequences plus isoforms. Synonyms and historical names persist in the literature, requiring cross-reference to avoid misidentification.

Challenges include cross-species differences, expanding gene families, and legacy naming. Researchers should use unambiguous identifiers (gene symbol, UniProt accession) alongside a common protein name. Cross-database mappings and controlled vocabularies help maintain consistency across datasets and publications.

Key resources for proteinnaming include UniProt, NCBI Gene and Protein, HGNC, ENSEMBL, IUBMB's Enzyme Nomenclature, and domain databases such as Pfam. These resources provide approved names, synonyms, and accession numbers to support standardized annotation.