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Introduction
KBDOCK is a 3D database system that defines and spatially clusters protein
binding sites for knowledge-based protein docking.
KBDOCK integrates protein domain-domain interaction information from
3DID
and sequence alignments from
PFAM
together with structural information from the
PDB
in order to analyse the spatial arrangements of DDIs by Pfam family,
and to propose structural templates for protein docking.
Given a query Pfam domain, KBDOCK shows:
- a non-redundant list of hetero DDIs involving the query domain,
grouped by their binding site.
- a Jmol view showing the DDIs placed in the coordinate frame of the query domain.
You can choose to view one DDI at a time or a group of DDIs which share a similar
binding site according to our interface vector algorithm (see references).
- a Pfam consensus-based sequence alignment of the domains.
Each sequence is annotated with core and rim interacting residues,
and also the binding site centre residue.
Given two query domain structures, if FH† DDI templates exist in KBDOCK,
then for each distinct interface, KBDOCK provides:
- the best FH template (based on overall sequence identity) and
the corresponding docking model.
- a Jmol view of the query domains superposed onto the FH template.
- a pairwise sequence alignment of the query domains and their corresponding
template domain, showing the core, rim, and centre binding site residues.
If FH DDIs do not exist or if only one query domain structure is given,
KBDOCK finds SH‡ DDI templates.
For each query domain and for each distinct binding site, it provides:
- the best SH template (based on domain sequence identity).
- a Jmol view of the query domain superposed onto the SH template.
A centre binding site residue is proposed.
- a pairwise sequence alignment of the query domain and its corresponding
template domain, showing the core, rim, and centre binding site residues.
†An FH DDI involves the same Pfam families as the query domains
‡An SH DDI involves one of the query domains
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People
Anisah Ghoorah
is a PhD student at the
INRIA
research centre
and her project involves the application of KDD to
protein-protein interaction data to guide protein docking calculations.
Email: anisah.ghoorah AT inria.fr
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Marie-Dominique Devignes
is a
CNRS Research Associate.
Email: devignes AT loria.fr
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Malika Smaïl-Tabbone
is an associate professor at Nancy-Université.
Her research interests include data integration, applications of data mining in biology, and relational data mining.
Email: malika AT loria.fr
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Dave Ritchie
is an
INRIA
Research Director. His research interests include protein docking, protein shape analysis, and virtual screening.
Email: dave.ritchie AT inria.fr
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Group and Lab
Orpailleur Team
Laboratoire Lorrain de Recherche en Informatique et ses Applications
(LORIA), France
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