title: KBDOCK 2013: a spatial classification of 3D protein domain family interactions.
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.
authors.affiliation: Université de Lorraine, LORIA, Campus Scientifique, BP 239, 54506 Villers-lès-Nancy, France, CNRS, LORIA, Campus Scientifique, BP 239, 54506 Villers-lès-Nancy, France and INRIA Nancy Grand Est, LORIA, Campus Scientifique, BP 239, 54506 Villers-lès-Nancy, France.
authors.forename: Anisah W
authors.initials: AW
authors.lastname: Ghoorah
authors.forename: Marie-Dominique
authors.initials: MD
authors.lastname: Devignes
authors.forename: Malika
authors.initials: M
authors.lastname: Smaïl-Tabbone
authors.forename: David W
authors.initials: DW
authors.lastname: Ritchie
mesh_terms: D001665:Binding Sites; D030562:Databases, Protein; D020407:Internet; D008958:Models, Molecular; D062105:Molecular Docking Simulation; D054730:Protein Interaction Domains and Motifs; D025941:Protein Interaction Mapping; D060066:Protein Interaction Maps; D011506:Proteins / Q000145:classification; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein
chemical_list: D011506:Proteins