Classification and Exploration of 3D Protein Domain Interactions Using Kbdock.
Comparing and classifying protein domain interactions according to their three-dimensional (3D) structures can help to understand protein structure-function and evolutionary relationships. Additionally, structural knowledge of existing domain-domain interactions can provide a useful way to find structural templates with which to model the 3D structures of unsolved protein complexes. Here we present a straightforward guide to using the "Kbdock" protein domain structure database and its associated web site for exploring and comparing protein domain-domain interactions (DDIs) and domain-peptide interactions (DPIs) at the Pfam domain family level. We also briefly explain how the Kbdock web site works, and we provide some notes and suggestions which should help to avoid some common pitfalls when working with 3D protein domain structures.
Department of Computer Science and Engineering, University of Mauritius, 80837, Reduit, Mauritius.
Anisah W
AW
Ghoorah
CNRS, LORIA, Campus Scientifique, BP 239, 54506, Vandoeuvre-lès-Nancy, France.
Marie-Dominique
MD
Devignes
University of Lorraine, LORIA, Campus Scientifique, BP 239, 54506, Vandoeuvre-lès-Nancy, France.
Malika
M
Smaïl-Tabbone
Inria Nancy - Grand Est, 615 Rue Du Jardin Botanique, 54600, Villers-lès-Nancy, France. dave.ritchie@inria.fr.
David W
DW
Ritchie
D030562:Databases, Protein; D020407:Internet; D008958:Models, Molecular; D062105:Molecular Docking Simulation; D011485:Protein Binding; D000072417:Protein Domains; D054730:Protein Interaction Domains and Motifs; D060066:Protein Interaction Maps; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*
D011506:Proteins
Domain family binding sites; Domain family interactions; Domain–domain interactions; Domain–peptide interactions; Protein domain family; Protein domains; Structural biology; Structural homology