Macromolecular complexes—those stable assemblies formed by multiple polypeptide chains—constitute the machineries that drive and regulate a large proportion of cellular processes. They bring together molecules involved in a shared function, structure disordered regions of proteins, or create new binding sites at the interfaces between subunits. Until now, however, the specific catalogues of these complexes were either irregularly maintained or assembled entry by entry from isolated articles rather than from consolidated knowledge. The Complex Portal was developed to fill this gap: it is an encyclopaedic, entirely manually curated database that catalogues the composition, topology and function of known macromolecular complexes across several model organisms, linking them to specialised resources such as wwPDB, EMDB and Reactome.
Since the previous update in 2019, coverage has expanded markedly. The authors have produced a first draft of the Escherichia coli complexome, while maintaining and enriching that of Saccharomyces cerevisiae as new experimental data identify previously unknown assemblies. In response to the SARS-CoV-2 pandemic, more than forty coronavirus complexes have been added. The human complexome now exceeds 1100 complexes, of which approximately 200 serve as targets for viral proteins or participate in the immune system. As of release 241 (October 2021), 3572 complexes from 26 species had been curated.
In terms of tools, the display of protein features in ComplexViewer has been improved to present multiple properties simultaneously and to visualise the links between participants of sub-complexes; the participant table now adopts a colour code consistent with the nodes of the viewer. The ComplexTab format has acquired a dedicated column for UniProt identifiers only. Community collaborations have also broadened: contribution to a large-scale analysis of putative transcription cofactors, development of a bot populating Wikidata with the curated content of the Complex Portal to make it accessible to semantic web tools, and integration of the entries as a new ontology in the ClueGO application of Cytoscape for enrichment analyses. This integration into Wikidata, initiated during a COVID-19 hackathon, has made it possible to directly link complex identifiers to the WikiPathways and COVID-19 Disease Map projects.
Finally, the data licence has been changed to CC0 to promote reuse. Work is now focused on completing a first version of the human complexome, with particular attention to immune system complexes, and on developing import pipelines from PDBe to accelerate curation. The authors invite users to submit their feedback and curation requests via the support page.