Classification and Exploration of 3D Protein Domain Interactions Using Kbdock

Anisah Ghoorah 1 Marie-Dominique Devignes 2 Malika Smaïl-Tabbone 3 David Ritchie 2
2 CAPSID - Computational Algorithms for Protein Structures and Interactions
Inria Nancy - Grand Est, LORIA - AIS - Department of Complex Systems, Artificial Intelligence & Robotics
3 ORPAILLEUR - Knowledge representation, reasonning
Inria Nancy - Grand Est, LORIA - NLPKD - Department of Natural Language Processing & Knowledge Discovery
Abstract : 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.
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Anisah 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⟩

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