Complex Portal


30357405	Complex Portal 2018: extended content and enhanced visualization tools for macromolecular complexes. [PMID: 30357405] Meldal BHM, Bye-A-Jee H, Gajdoš L, Hammerová Z, Horácková A, Melicher F, Perfetto L, Pokorný D, Lopez MR, Türková A, Wong ED, Xie Z, Casanova EB, Del-Toro N, Koch M, Porras P, Hermjakob H, Orchard S. Abstract The Complex Portal (www.ebi.ac.uk/complexportal) is a manually curated, encyclopaedic database that collates and summarizes information on stable, macromolecular complexes of known function. It captures complex composition, topology and function and links out to a large range of domain-specific resources that hold more detailed data, such as PDB or Reactome. We have made several significant improvements since our last update, including improving compliance to the FAIR data principles by providing complex-specific, stable identifiers that include versioning. Protein complexes are now available from 20 species for download in standards-compliant formats such as PSI-XML, MI-JSON and ComplexTAB or can be accessed via an improved REST API. A component-based JS front-end framework has been implemented to drive a new website and this has allowed the use of APIs from linked services to import and visualize information such as the 3D structure of protein complexes, its role in reactions and pathways and the co-expression of complex components in the tissues of multi-cellular organisms. A first draft of the complete complexome of Saccharomyces cerevisiae is now available to browse and download. Nucleic Acids Res. 2019:47(D1) \| 63 Citations (from Europe PMC, 2025-03-29)
25313161	The complex portal--an encyclopaedia of macromolecular complexes. [PMID: 25313161] Meldal BH, Forner-Martinez O, Costanzo MC, Dana J, Demeter J, Dumousseau M, Dwight SS, Gaulton A, Licata L, Melidoni AN, Ricard-Blum S, Roechert B, Skyzypek MS, Tiwari M, Velankar S, Wong ED, Hermjakob H, Orchard S. Abstract The IntAct molecular interaction database has created a new, free, open-source, manually curated resource, the Complex Portal (www.ebi.ac.uk/intact/complex), through which protein complexes from major model organisms are being collated and made available for search, viewing and download. It has been built in close collaboration with other bioinformatics services and populated with data from ChEMBL, MatrixDB, PDBe, Reactome and UniProtKB. Each entry contains information about the participating molecules (including small molecules and nucleic acids), their stoichiometry, topology and structural assembly. Complexes are annotated with details about their function, properties and complex-specific Gene Ontology (GO) terms. Consistent nomenclature is used throughout the resource with systematic names, recommended names and a list of synonyms all provided. The use of the Evidence Code Ontology allows us to indicate for which entries direct experimental evidence is available or if the complex has been inferred based on homology or orthology. The data are searchable using standard identifiers, such as UniProt, ChEBI and GO IDs, protein, gene and complex names or synonyms. This reference resource will be maintained and grow to encompass an increasing number of organisms. Input from groups and individuals with specific areas of expertise is welcome. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research. Nucleic Acids Res. 2015:43(Database issue) \| 56 Citations (from Europe PMC, 2025-03-29)

Complex Portal 2018: extended content and enhanced visualization tools for macromolecular complexes. [PMID: 30357405]

Meldal BHM, Bye-A-Jee H, Gajdoš L, Hammerová Z, Horácková A, Melicher F, Perfetto L, Pokorný D, Lopez MR, Türková A, Wong ED, Xie Z, Casanova EB, Del-Toro N, Koch M, Porras P, Hermjakob H, Orchard S.

Abstract

The Complex Portal (www.ebi.ac.uk/complexportal) is a manually curated, encyclopaedic database that collates and summarizes information on stable, macromolecular complexes of known function. It captures complex composition, topology and function and links out to a large range of domain-specific resources that hold more detailed data, such as PDB or Reactome. We have made several significant improvements since our last update, including improving compliance to the FAIR data principles by providing complex-specific, stable identifiers that include versioning. Protein complexes are now available from 20 species for download in standards-compliant formats such as PSI-XML, MI-JSON and ComplexTAB or can be accessed via an improved REST API. A component-based JS front-end framework has been implemented to drive a new website and this has allowed the use of APIs from linked services to import and visualize information such as the 3D structure of protein complexes, its role in reactions and pathways and the co-expression of complex components in the tissues of multi-cellular organisms. A first draft of the complete complexome of Saccharomyces cerevisiae is now available to browse and download.

Nucleic Acids Res. 2019:47(D1) | 63 Citations (from Europe PMC, 2025-03-29)

The complex portal--an encyclopaedia of macromolecular complexes. [PMID: 25313161]

Meldal BH, Forner-Martinez O, Costanzo MC, Dana J, Demeter J, Dumousseau M, Dwight SS, Gaulton A, Licata L, Melidoni AN, Ricard-Blum S, Roechert B, Skyzypek MS, Tiwari M, Velankar S, Wong ED, Hermjakob H, Orchard S.

Abstract

The IntAct molecular interaction database has created a new, free, open-source, manually curated resource, the Complex Portal (www.ebi.ac.uk/intact/complex), through which protein complexes from major model organisms are being collated and made available for search, viewing and download. It has been built in close collaboration with other bioinformatics services and populated with data from ChEMBL, MatrixDB, PDBe, Reactome and UniProtKB. Each entry contains information about the participating molecules (including small molecules and nucleic acids), their stoichiometry, topology and structural assembly. Complexes are annotated with details about their function, properties and complex-specific Gene Ontology (GO) terms. Consistent nomenclature is used throughout the resource with systematic names, recommended names and a list of synonyms all provided. The use of the Evidence Code Ontology allows us to indicate for which entries direct experimental evidence is available or if the complex has been inferred based on homology or orthology. The data are searchable using standard identifiers, such as UniProt, ChEBI and GO IDs, protein, gene and complex names or synonyms. This reference resource will be maintained and grow to encompass an increasing number of organisms. Input from groups and individuals with specific areas of expertise is welcome. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Nucleic Acids Res. 2015:43(Database issue) | 56 Citations (from Europe PMC, 2025-03-29)

URL:	http://www.ebi.ac.uk/complexportal/
Full name:
Description:	A manually curated, encyclopaedic resource of macromolecular complexes from model organisms.
Year founded:	2015
Last update:	2018
Version:	v1.0
Accessibility:	Accessible
Country/Region:	United Kingdom

Data type:	Protein
Data object:	Animal Bacteria Fungi Plant Virus
Database category:	Interaction
Major species:	Homo sapiens Mus musculus Rattus norvegicus Caenorhabditis elegans Gallus gallus Arabidopsis thaliana Saccharomyces cerevisiae Escherichia coli Drosophila melanogaster Schizosaccharomyces pombe Bos taurus Danio rerio Oryctolagus cuniculus Xenopus laevis Sus scrofa Canis lupus Pseudomonas aeruginosa Lymnaea stagnalis Tetronarce californica Torpedo marmorata
Keywords:	macromolecular complex gene ontology model organism protein interactions systems biology SARS-CoV-2

University/Institution:	European Bioinformatics Institute
Address:	Hinxton, Cambridge CB10 1SD, UK
City:	Cambridge
Province/State:	Cambridgeshire
Country/Region:	United Kingdom
Contact name (PI/Team):	Henning Hermjakob
Contact email (PI/Helpdesk):	complexportal@ebi.ac.uk

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Database Commons a catalog of worldwide biological databases