ArticleNucleic acids research2011
3did: identification and classification of domain-based interactions of known three-dimensional structure.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 62 papers.
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Who cites it
62 citing papers in PubMed.
- Proteoform medicine: characterizing and targeting protein forms in human disease.Nature reviews. Genetics · 2026Review
- Generation of a high confidence set of domain-domain interface types to guide protein complex structure predictions by AlphaFold.Bioinformatics (Oxford, England) · 2024Article
- PPIDomainMiner: Inferring domain-domain interactions from multiple sources of protein-protein interactions.PLoS computational biology · 2021Article
- The carboxy-terminus, a key regulator of protein function.Critical reviews in biochemistry and molecular biology · 2019Review
- Pattern to Knowledge: Deep Knowledge-Directed Machine Learning for Residue-Residue Interaction Prediction.Scientific reports · 2018Article
- Perturbed human sub-networks by Fusobacterium nucleatum candidate virulence proteins.Microbiome · 2017Article
- Enhancing interacting residue prediction with integrated contact matrix prediction in protein-protein interaction.EURASIP journal on bioinformatics & systems biology · 2016Article
- DOMMINO 2.0: integrating structurally resolved protein-, RNA-, and DNA-mediated macromolecular interactions.Database : the journal of biological databases and curation · 2016Article
- Network-Based Isoform Quantification with RNA-Seq Data for Cancer Transcriptome Analysis.PLoS computational biology · 2015Article
- Flexibility and small pockets at protein-protein interfaces: New insights into druggability.Progress in biophysics and molecular biology · 2015Review
- Surfing the Protein-Protein Interaction Surface Using Docking Methods: Application to the Design of PPI Inhibitors.Molecules (Basel, Switzerland) · 2015Review
- Prediction of host - pathogen protein interactions between Mycobacterium tuberculosis and Homo sapiens using sequence motifs.BMC bioinformatics · 2015Article
- Mechismo: predicting the mechanistic impact of mutations and modifications on molecular interactions.Nucleic acids research · 2015Article
- K-core decomposition of a protein domain co-occurrence network reveals lower cancer mutation rates for interior cores.Journal of clinical bioinformatics · 2015Article
- Algorithmic approaches to protein-protein interaction site prediction.Algorithms for molecular biology : AMB · 2015Article
- A massively parallel pipeline to clone DNA variants and examine molecular phenotypes of human disease mutations.PLoS genetics · 2014Article
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- Classification of intrinsically disordered regions and proteins.Chemical reviews · 2014Review
- Homology-based prediction of interactions between proteins using Averaged One-Dependence Estimators.BMC bioinformatics · 2014Article
2 more citing papers are in PubMed but not listed here.
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3 authors.
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Abstract
The database of three-dimensional interacting domains (3did) is a collection of protein interactions for which high-resolution three-dimensional structures are known. 3did exploits the availability of structural data to provide molecular details on interactions between two globular domains as well as novel domain-peptide interactions, derived using a recently published method from our lab. The interface residues are presented for each interaction type individually, plus global domain interfaces at which one or more partners (domains or peptides) bind. The 3did web server at http://3did.irbbarcelona.org visualizes these interfaces along with atomic details of individual interactions using Jmol. The complete contents are also available for download.
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