ArticleNucleic acids research2014
KBDOCK 2013: a spatial classification of 3D protein domain family interactions.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- DIGGER 2.0: digging into the functional impact of differential splicing on human and mouse disorders.Nucleic acids research · 2025Article
- Review
- PPIDomainMiner: Inferring domain-domain interactions from multiple sources of protein-protein interactions.PLoS computational biology · 2021Article
- InterEvDock3: a combined template-based and free docking server with increased performance through explicit modeling of complex homologs and integration of covariation-based contact maps.Nucleic acids research · 2021Article
- 3D-PP: A Tool for Discovering Conserved Three-Dimensional Protein Patterns.International journal of molecular sciences · 2019Article
- PHI-Nets: A Network Resource for Ascomycete Fungal Pathogens to Annotate and Identify Putative Virulence Interacting Proteins and siRNA Targets.Frontiers in microbiology · 2019Article
- The CYP71AZ P450 Subfamily: A Driving Factor for the Diversification of Coumarin Biosynthesis in Apiaceous Plants.Frontiers in plant science · 2018Article
- Large oligomeric complex structures can be computationally assembled by efficiently combining docked interfaces.Proteins · 2015Article
- Surfing the Protein-Protein Interaction Surface Using Docking Methods: Application to the Design of PPI Inhibitors.Molecules (Basel, Switzerland) · 2015Review
- A structure-based classification and analysis of protein domain family binding sites and their interactions.Biology · 2015Article
- Drug-Like Protein-Protein Interaction Modulators: Challenges and Opportunities for Drug Discovery and Chemical Biology.Molecular informatics · 2014Review
- Peptides encoded by noncoding genes: challenges and perspectives.Signal transduction and targeted therapyReview
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Comparing, classifying and modelling protein structural interactions can enrich our understanding of many biomolecular processes. This contribution describes Kbdock (http://kbdock.loria.fr/), a database system that combines the Pfam domain classification with coordinate data from the PDB to analyse and model 3D domain-domain interactions (DDIs). Kbdock can be queried using Pfam domain identifiers, protein sequences or 3D protein structures. For a given query domain or pair of domains, Kbdock retrieves and displays a non-redundant list of homologous DDIs or domain-peptide interactions in a common coordinate frame. Kbdock may also be used to search for and visualize interactions involving different, but structurally similar, Pfam families. Thus, structural DDI templates may be proposed even when there is little or no sequence similarity to the query domains.
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Registered trials
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