PPIDomainMiner
A dataset of protein domain-domain interactions (DDIs) inferred from multiple sources of protein-protein interactions. The inference method is an extension of the generic CODAC (COmputational discovery of Direct Associations using Common neighbours) method. Recently published in PLOS Computational Biology (2021)
Go to PPIDM page.
Kbdock : 3D Domain-Domain interactions
Kbdock is a database of protein domain interactions extracted from the Protein Data Bank (PDB). Domain-domain interactions can be searched by Pfam identifier(s). The interaction partners for a particular domain of interest are set in a common coordinate frame before clustering the binding sites, thereby defining domain family binding sites (DFBS, see the reference papers: Bioinformatics,2011 or NAR,2013). Kbdock was developed by Anisah Ghoorah during her PhD at the Loria (2009-2013) and updated by Zia Alborzi during his PhD at the Loria (2014-2018)
Go to the Kbdock main page.
Characterization of protein domains
ECDomainMiner
A dataset of protein domains (from the Pfam classification) with automatically inferred functional annotations : EC (Enzyme Commission) numbers. The inference method is inspired by recommendation systems and described in this publication.
Go to ECDM website.
GODomainMiner
A dataset of protein domains (from the Pfam classification) with automatically inferred functional annotations : GO (Gene Ontology) terms. The inference method is the generic CODAC (COmputational discovery of Direct Associations using Common neighbours) method described in this publication.
Go to GODM website.
Virtual Screening
Galaxy
Galaxy is an open, web-based platform for data intensive research in bioinformatics. Whether on a free public server or a local instance, it can perform, reproduce, and share complete analyses.
Within the scope of the MBI platform a local instance of Galaxy was implemented to share specific tools and workflows in structural bioinformatics, especially for virtual screening. However the access to this local instance is restricted to collaborators having an account on the MBI-DS4H platform. Ask for an account here.
VSM-G3 : Virtual Screening Manager for running Gold on the Grid under Galaxy environment.
The VSM-G3 project benefited in 2021-2023 of an INRIA ADT (Action de Développement Technologique). Engineer Oliver Demengeon has been the linchpin of this project, which now allows researchers to focus their efforts on expert analysis and interpretation of docking results.
GOLD is the ligand docking program developped and distributed by Cambridge Crystallographic Data Centre.
The Grid is composed of a set of MBI-DS4H machines on which the GOLD licence was installed .
Galaxy is a generic web platform for running programs and building workflows in a FAIR environment. It provides a user-friendly interface and facilities for job management. At the back-end, it allows to interface any encapsulated program and to manage job executions.
See VSM-G3 report, december 2023.
