Classification and Exploration of 3D Protein Domain Interactions Using Kbdock

Anisah W Ghoorah (1) , Marie-Dominique Devignes (2) , Malika Smaïl-Tabbone (3) , David Ritchie (2)

1 University of Mauritius
2 CAPSID - Computational Algorithms for Protein Structures and Interactions
3 ORPAILLEUR - Knowledge representation, reasonning

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.

Mots clés: Structural biology; Structural homology; Protein domains; Protein domain family; Domain–domain interactions

Domaines: Bio-informatique [q-bio.QM]

Anisah W Ghoorah, Marie-Dominique Devignes, Malika Smaïl-Tabbone, David Ritchie. Classification and Exploration of 3D Protein Domain Interactions Using Kbdock. O. Carugo; F. Eisenhaber. Data Mining Techniques for the Life Sciences, 1415, Springer Science+Business Media New York, pp.91-105, 2016, Methods in Molecular Biology, 978-1-4939-3570-3. ⟨10.1007/978-1-4939-3572-7_5⟩. ⟨hal-01317448⟩