Introduction

KBDOCK is a 3D database system that defines and spatially clusters protein binding sites for knowledge-based protein docking. KBDOCK extracts protein domain-domain interaction (DDI) and domain-peptide interaction (DPI) information from the PDB using the PFAM domain classification in order to analyse the spatial arrangements of DDIs and DPIs by Pfam family, and to propose structural templates for protein docking.

Given a query Pfam domain, KBDOCK shows:

Given a query Pfam domain, KBDOCK can also show DDIs involving different but structurally similar Pfam domains. For each Pfam family, KBDOCK stores a list of "Pfam neighbours" which is calculated using the Kpax structure alignment algorithm.

Given two query domain structures, if full-homology (FH) DDI templates exist in KBDOCK, then for each distinct interface, KBDOCK provides:

If FH DDIs do not exist or if only one query domain structure is given, KBDOCK finds semi-homology (SH) DDI templates. For each query domain and for each distinct binding site, it provides:

KBDOCK can also find DDIs involving structurally similar Pfam domains to the query domains using pre-calculated Pfam neighbour lists.

An FH DDI involves the same Pfam families as the query domains
  An SH DDI involves one of the query domains

References

KBDOCK 2013: A spatial classification of 3D protein domain family interactions.
Ghoorah A.W., Smaïl-Tabbone M., Devignes M-D., and Ritchie D.W.
Nucleic Acids Research, 2014, 42:D389-D395 [PDF]

Protein Docking Using Case-Based Reasoning.
Ghoorah A.W., Smaïl-Tabbone M., Devignes M-D., and Ritchie D.W.
Proteins, 2013, 81:2150-2158 [DOI]

Spatial clustering of protein binding sites for template-based protein docking.
Ghoorah A.W., Devignes M-D., Smaïl-Tabbone M., and Ritchie D.W.
Bioinformatics 2011 27(20):2820-7 [Pre-print PDF]

Fast protein structure alignment using Gaussian overlap scoring of backbone peptide fragment similarity.
Ritchie D.W, Ghoorah A.W, Mavridis L., Venkatraman V.
Bioinformatics 2012 28(24):3274-3281 [PDF]
http://kpax.loria.fr/

People

Group and Lab

Orpailleur Team, Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), France

Acknowledgements

Agence Nationale de la Recherche, France, grant reference:
ANR-08-CEXC-017-01 (2009-2011) and ANR-11-MONU-006-02 (2011-2012)