Interactome3D: adding structural details to protein networks
Open accessAbstract
Network-centered approaches are increasingly used to understand the fundamentals of biology. However, the molecular details contained in the interaction networks, often necessary to understand cellular processes, are very limited, and the experimental difficulties surrounding the determination of protein complex structures make computational modeling techniques paramount. Here we present Interactome3D, a resource for the structural annotation and modeling of protein-protein interactions. Through the integration of interaction data from the main pathway repositories, we provide structural details at atomic resolution for over 12,000 protein-protein interactions in eight model organisms. Unlike static databases, Interactome3D also allows biologists to upload newly discovered interactions and pathways in any species, select the best combination of structural templates and build three-dimensional models in a fully automated manner. Finally, we illustrate the value of Interactome3D through the structural annotation of the complement cascade pathway, rationalizing a potential common mechanism of action suggested for several disease-causing mutations.
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A complementary multiscale visualization strategy is to integrate 3D structural information with associated nodes in a hierarchy; software tools have been developed that display available 3D structural data for selected proteins and physical pairwise interactions in protein-protein interaction networks.
“A complementary multiscale visualization strategy is to integrate 3D structural information with associated nodes in a hierarchy; software tools have been developed that display available 3D structural data for selected proteins and physical pairwise interactions in protein-protein interaction networks (Morris et al., 2007; Mosca et al., 2013; Nepomnyachiy et al., 2015).”
From Mapping the multiscale structure of biological systems (2021) · cites this paper as Mosca et al., 2013
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- Authors
- Mosca, R., Céol, A., & Aloy, P.
- Affiliations
- Institute for Research in Biomedicine (ES)
- Institució Catalana de Recerca i Estudis Avançats (ES)
- Corresponding author
- Aloy, Patrick
- Venue
- Nature Methods
- Published
- 2013-01
- Volume
- 10
- Issue
- 1
- Pages
- 47-53
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- OpenAlex
- W1965379872
- Cited by
- 479
- References
- 69
- Citations by year
- 2026: 17 · 2025: 15 · 2024: 24 · 2023: 45 · 2022: 34 · 2021: 50 · 2020: 45 · 2019: 45 · 2018: 44 · 2017: 39 · 2016: 33 · 2015: 32 · 2014: 27 · 2013: 28 · 2012: 1
- FWCI
- 11.30
- Type
- journal article
- Language
- en
- Open access
- green
- zenodo.org
- Licence
- Locations
- Nature Methods (publishedVersion)
- PubMed (publishedVersion)
- Zenodo (CERN European Organization for Nuclear Research) (submittedVersion, other-oa)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Keywords
- protein-protein interaction, protein-protein interaction network, structural annotation, protein complex structure, automated 3D modeling, structural templates, complement system, pathogenic variants
- MeSH terms
- Animals, Computer Simulation, Humans, Models, Biological, Protein Conformation, Proteins, Protein Interaction Mapping, Databases, Protein, Multiprotein Complexes
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