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. 2022 Jan 7;50(D1):D648-D653.
doi: 10.1093/nar/gkab1006.

The IntAct database: efficient access to fine-grained molecular interaction data

Noemi Del Toro  1 , Anjali Shrivastava  1 , Eliot Ragueneau  1 , Birgit Meldal  1 , Colin Combe  2 , Elisabet Barrera  1 , Livia Perfetto  1   3 , Karyn How  4 , Prashansa Ratan  4 , Gautam Shirodkar  4 , Odilia Lu  4 , Bálint Mészáros  5 , Xavier Watkins  1 , Sangya Pundir  1 , Luana Licata  6 , Marta Iannuccelli  6 , Matteo Pellegrini  7 , Maria Jesus Martin  1 , Simona Panni  8 , Margaret Duesbury  1   4 , Sylvain D Vallet  9 , Juri Rappsilber  2   10 , Sylvie Ricard-Blum  9 , Gianni Cesareni  6 , Lukasz Salwinski  4 , Sandra Orchard  1 , Pablo Porras  1 , Kalpana Panneerselvam  1 , Henning Hermjakob  1
Affiliations

The IntAct database: efficient access to fine-grained molecular interaction data

Noemi Del Toro et al. Nucleic Acids Res. .

Abstract

The IntAct molecular interaction database (https://www.ebi.ac.uk/intact) is a curated resource of molecular interactions, derived from the scientific literature and from direct data depositions. As of August 2021, IntAct provides more than one million binary interactions, curated by twelve global partners of the International Molecular Exchange consortium, for which the IntAct database provides a shared curation and dissemination platform. The IMEx curation policy has always emphasised a fine-grained data and curation model, aiming to capture the relevant experimental detail essential for the interpretation of the provided molecular interaction data. Here, we present recent curation focus and progress, as well as a completely redeveloped website which presents IntAct data in a much more user-friendly and detailed way.

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Figures

Figure 1.
Figure 1.
IntAct search results for UniProtKB:P0C6 × 7-PRO_0000037322. The option ‘Affected by Mutation’ has been selected in facet (A), highlighting corresponding interactions in bold pink. The minimum MI score (label B) has been set to 0.43. One interaction between SARS-CoV proteins, nsp10-nsp16 is highlighted (through mouse click) in purple (edge C). The interaction table (D) automatically shows only the highlighted interaction. The legend on the right (E) documents the representation of species, type of biomolecule, mutations and edge types. Clicking on the magnifying glass (icon F) provides detailed information on an interaction, as shown in Figure 2. Interactor positions can be manually rearranged through drag-and-drop, as done here. Figure is a modified screen capture from.https://www.ebi.ac.uk/intact/search?query=P0C6X7-PRO_0000037322&minMIScore=0.43&mutationStyle=true.
Figure 2.
Figure 2.
This figure shows the interaction viewer for the highlighted edge from Figure 1. Features of the participants including the N-terminal tags (A) and all the mutations annotated for this interaction are displayed in the viewer (B) and also in the legend (C). All the features are mapped at the amino acid level of the proteins. Further details on the features are available from the features tab (D) below the Interaction viewer. Figure is a modified screen capture from https://www.ebi.ac.uk/intact/details/interaction/EBI-25506442.
Figure 3.
Figure 3.
Species-specific interactomes are easily accessible from the ‘Interactomes’ tile of the home page.
See this image and copyright information in PMC

References

    1. Orchard S., Kerrien S., Abbani S., Aranda B., Bhate J., Bidwell S., Bridge A., Briganti L., Brinkman F.S.L., Cesareni G.et al. .. Protein interaction data curation: the International Molecular Exchange (IMEx) consortium. Nat. Methods. 2012; 9:345–350. - PMC - PubMed
    1. Drysdale R., Cook C.E., Petryszak R., Baillie-Gerritsen V., Barlow M., Gasteiger E., Gruhl F., Haas J., Lanfear J., Lopez R.et al. .. The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences. Bioinformatics. 2020; 36:2636–2642. - PMC - PubMed
    1. Porras P., Barrera E., Bridge A., Del-Toro N., Cesareni G., Duesbury M., Hermjakob H., Iannuccelli M., Jurisica I., Kotlyar M.et al. .. Towards a unified open access dataset of molecular interactions. Nat. Commun. 2020; 11:6144. - PMC - PubMed
    1. Salwinski L., Miller C.S., Smith A.J., Pettit F.K., Bowie J.U., Eisenberg D. The Database of Interacting Proteins: 2004 update. Nucleic Acids Res. 2004; 32:D449–D451. - PMC - PubMed
    1. UniProt Consortium UniProt: the universal protein knowledgebase in 2021. Nucleic Acids Res. 2021; 49:D480–D489. - PMC - PubMed

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