MBI

Adress
615 Rue du Jardin Botanique 54600 Villers-lès-Nancy
Structure(s)
INRIA
Unit:
Inria Nancy Grand-Est
Regional Center
IFB North East
Website
LORIA
Scientific leader
Devignes Marie Dominique
Technical leader
Ritchie Dave
Certificat(s)
Not documented
Infrastructure
Propriétaire
Effective storage
80.00 To
Cluster: cores number
300 cores
Users number (last year)
25
Servers description

Cluster : 300 CPU cores (2.4 GHz Intel Xeon) + 8 GPU (Nvidia Tesla K40M)

Databases : MySQL, PostgreSQL

Tools : NAMD, Autodock, Gold, Hex, Parafit, KBDOCK, Kpax, ECDomainMiner, Coron, Knime


Access conditions

Compte local requis pour faire tourner les calculs lourds ou les logiciels commerciaux ; libre accès externe pour Hex, KBDOCK, Kpax

Annual visits:
3 600 an
Unique visits:
Not documented
Quotes:
36
Latest update:
18-01-2017

KBDOCK

Description

3D database system that defines and spatially clusters protein binding sites for knowledge-based protein docking

Access conditions

Free service : no login or registration required.

Annual visits:
18 000 an
Unique visits:
5 000 an
Quotes:
720
Downloads:
43 000

Hex

Description

Ab initio rigid body protein-protein docking.

Access conditions

Free licence for academic use

Annual visits:
5 000 an
Unique visits:
Not documented
Quotes:
266
Downloads:
0

HexServer

Description

Ab initio rigid body protein-protein docking using GPU.

Access conditions

Free service: no login or registration required

Annual visits:
400 an
Unique visits:
50 an
Quotes:
15
Downloads:
200

Kpax

Description

Fast protein structure alignment (pairwise, multiple, flexible) and database search (e.g. CATH, SCOP, ECOD, Pfam).

Access conditions

No-cost licence for academic use.

Domains of activity
  • Biomedical
  • Biology
Description of expertise domains
Plateforme expérimentale de recherche dépendant de Inria Nancy Grand-Est, la plateforme MBI s’est constituée autour de deux domaines principaux d’expertise.

1. La modélisation 3D des protéines et de leurs interactions, avec en particulier la simulation de dynamiques moléculaires (logiciel NAMD), et la mise à disposition de programmes ultra-rapides de docking rigide et de comparaison de formes, exécutés sur des clusters mixtes (CPU et GPU).

2. L’extraction de connaissances à partir de données biologiques ou biomédicales, avec en particulier la mise en œuvre de méthodes de fouille de données symboliques et/ou relationnelles, en utilisant une suite logicielle construite dans l’équipe Orpailleur autour de la recherche de motifs fréquents et de l’analyse formelle de concept (suite CORON), ainsi que des workflows d’apprentissage (à partir de la plateforme KNIME).

Keywords:
  • Structural bioinformatics
  • Modelling of proteins/proteins, proteins/peptides and proteines/nucleic acids interactions
Users distribution
International
20 %
National
10 %
Regional
10 %
Local
60%
Explanation about this distribution:

Ces chiffres sont des estimations car aucun login n'est nécessaire pour utiliser Hex ou KBDOCK, par exemple, qui sont principalement utilisés par des utilisateurs externes.

Platform's own projects

Mise en place de l'environnement de travail Galaxy (CDD IFB Antoine Chemardin)

Collaborations
National projets
(1)

ANR: ANR-11-MONU-006-01/2/3 to: S. Grudinin, D.W. Ritchie, V. Gordeliy, 01/11/11-30/10/15, €358K. PEPSI – Expansions Polynomiales de Structures de Protéines et Interactions.

International and European projects
(1)

Collaboration avec le Brésil (via l'accueil de doctorants et de chercheurs invités pour travailler 1 à 6 mois sur la plateforme MBI): University of Mato Grosso State, University of Maringá, Embrapa, and University of Brasilia. Criblage virtuel de molécules anti-fongiques.

Projets with industry
(1)

Collaboration avec la start-up Harmonic Pharma qui utilise ponctuellement les ressources de calcul, dans le cadre des projets BioProLor (Projet AME Lorraine : 2009-2013) et Le Bois Santé (projet FUI-14 : 2013-2015).

Collaboration projects not founded through an external organism
Not documented
Provision of services not founded through an external organism
Not documented
Animations (Workshops, Work-groups, seminars, conferences ... )
Démonstration de docking proteine-proteine au Village des Sciences, 2014

Organised conference : SFCi 2013 6èmes journées de la Société Française de Chémoinformatique
(SFCi) http://sfci2013.loria.fr/

Organised workshop : Journée Charles Hermite – Inférence Ancestrale et Relations Évolutives en
Biologie http://www.fr-hermite.univ-lorraine.fr/content/Journee-scientifique-FCH-...

Organised workshop : « Computational Challenges in Structural Biology »
http://ccsb2012.loria.fr/

Internal publications
External publications
A. K. Rodrigues Adabio, E. S. Kioshima, V. Leroux, N. F. Martins, B. Maigret, M. S. Soares Felipe, “Identification of New Antifungal Compounds Targeting Thioredoxin Reductase of Paracoccidioides Genus”, PloS One 10, 11, November 2015, p. e0142926.

 

R. Gerbier, V. Leroux, P. Couvineau, R. Alvear-Perez, B. Maigret, C. Llorens- Cortes, X. Iturrioz, “New structural insights into the apelin receptor: identification of key residues for apelin binding”, FASEB Journal 29, 1, January 2015, p. 314–322.

 

T. Bourquard, F. Landomiel, E. Reiter, P. Crépieux, D. W. Ritchie, J. Azé, A. Poupon, “Unraveling the molecular architecture of a G protein-coupled receptor/ - arrestin/Erk module complex”, Scientific Reports, June 2015, p. 5:10760. http://hal-lirmm.ccsd.cnrs.fr/lirmm-01162594.

 

Ferrari F, Paris C, Maigret B, Bidouil C, Delaunay S, Humeau C, Chevalot I. Molecular rules for chemo- and regio-selectivity of Candida antarctica lipase B in peptide acylation reactions. Journal of Molecular Catalysis B – Enzymatic. 2014 101:122-132.


de Almeida H, Bastos IMD, Ribeiro BM, Maigret B, Santana JM. New Binding Site Conformations of the Dengue Virus NS3 Protease Accessed by Molecular Dynamics Simulation. PloS One 8:e72402.

Abadio, AKR, Kioshuma ES, Martins NF, FreitasSM, Maigret B, Felipe MS. Small molecules inhibitors of Paracoccidioides lutzii thioredoxin reductase obtained by virtual screening, promising antifungals agents. Mycoses. 2012 55:103:104.

Abadio, AKR, Kioshuma ES, Teixier MM, Martins NF, FreitasSM, Maigret B, Felipe MSS. Comparative genomics allowed the identification of drug targets against human fungal pathogens. BMC Genomics, 2011 12:75

S. Roselli, A. Olry, S. Vautrin, O. Coriton, D.W. Ritchie, G. Galati, N. Navrot, C. Krieger, G. Vialart, H. Bergès, F. , Bourgaud, A. Hehn (2017). A bacterial artificial chromosome (BAC) genomic approach reveals partial clustering of the furanocoumarin pathway genes in parsnip. The Plant Journal, in press. DOI: 10.1111/tpj.13450.


C. Ambroset, C. Coluzzi, G. Guédon, M.-D. Devignes, V. Leroux, T. Lacroix, S. Payot, N. Leblond-Bourget. New Insights into the Classification and Integration Specificity of Streptococcus Integrative Conjugative Elements through Extensive Genome Exploration. Frontiers. Microbiology, 2016, 6:1483. DOI: 10.3389/FMICB.2015.01483.


E. Bresso, V. Leroux, M. Urban, K. E. Hammond-Kosack, B. Maigret, N. F. Martins. Structure-based virtual screening of hypothetical inhibitors of the enzyme longiborneol synthase—a potential target to reduce Fusarium head blight disease. Journal of Molecular Modeling, 2016, 22(7) DOI: 10.1007/s00894-016-3021-1.

 


M. Martins, E. Bresso, R. C. Togawa, M. Urban, J.  Antoniw, B. Maigret, K. Hammond-Kosack. Searching for Novel Targets to Control Wheat Head Blight Disease – Protein Identification, 3D Modeling and Virtual Screening, in Advances in Microbiology, 2016, 6(11): 811-830. DOI: 10.4236/aim.2016.611079.


H. De Almeida, V. Leroux, F. N. Motta, P. G Rellier, B. Maigret, J. M. Santana, I. M. D. Bastos. Identification of novel Trypanosoma cruzi prolyl oligopeptidase inhibitors by structure-based virtual screening. Journal of Computer-Aided Molecular Design, 2016 DOI: 10.1007/S10822-016-9985-1.

Publications with the hosting laboratory
A structure-based classification and analysis of protein domain family binding sites and their interactions. Ghoorah AW, Devignes MD, Alborzi SZ, Smaïl-Tabbone M, Ritchie DW. (2015) Biology (Basel) 4(2):327-43.

 

V. Pérez-Nueno, A. S. Karaboga, M. Souchet, D. Ritchie, “GESSE: Predicting Drug Side Effects from Drug–Target Relationships”, Journal of Chemical Information and Modeling 55, 9, August 2015, p. 1804–1823, https://hal.inria.fr/hal-01216493.

 

KBDOCK 2013: A spatial classification of 3D protein domain family interactions. A.W. Ghoorah, M.- D. Devignes, M. Smail-Tabbone, D.W. Ritchie, (2014).Nucleic Acids Research, D389-D395.

Protein Docking Using Case-Based Reasoning. A.W. Ghoorah, M. Smail-Tabbone, M.-D. Devignes, D.W. Ritchie, (2013). Proteins, 2150-2158

Fast Protein Structure Alignment using Gaussian Overlap Scoring of Backbone Peptide Fragment Similarity. D.W. Ritchie, A.W. Ghoorah, L. Mavridis, V. Venkatraman (2012). Bioinformatics, 28(24) 3274-3281

Functional classification of genes using semantic distance and fuzzy clustering approach: evaluation with reference sets and overlap analysis. Devignes MD, Benabderrahmane S, Smaïl- Tabbone M, Napoli A, Poch O. Int J Comput Biol Drug Des. 2012;5(3-4):245-60

Spatial clustering of protein binding sites for template based protein docking. A. Ghoorah, M.-D. Devignes, M. Smail-Tabbone, D.W. Ritchie (2011). Bioinformatics, 27, 2820-2827.

Benabderrahmane S, Smail-Tabbone M, Poch O, Napoli A, Devignes MD. IntelliGO: a new vector- based semantic similarity measure including annotation origin. BMC Bioinformatics. 2010 Dec 1;11:588

Macindoe G, Mavridis L, Venkatraman V, Devignes MD, Ritchie DW. HexServer: an FFT-based protein docking server powered by graphics processors. Nucleic Acids Res. 2010 Jul;38(Web Server issue):W445-9.

M. El Houasli, B. Maigret, M.-D. Devignes, A. W. Ghoorah, S. Grudinin, D.W. Ritchie (2016). Modeling and Minimising CAPRI Round 30 Symmetrical Protein Complexes from CASP-11 Structural Models. Proteins, Structure, Function, Bioinformatics, 2016, 84, in press. DOI: 10.1002/prot.25182.


A.W. Ghoorah, M.-D. Devignes, M. Smail-Tabbone, D.W. Ritchie. Classification and Exploration of 3D Protein Domain Interactions Using Kbdock. In Methods in Molecular Biology 1415 - Data Mining Techniques for the Life Sciences (Eds. O. Carugo and F. Eisenhaber), 2016, 2, 91-105.

Development
Nœuds KNIME MODIM
cea
cnrs
inra
inria
inserm
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