RPBS

Adress
35 rue Hélène Brion 75013 Paris
Structure(s)
INSERM, Université Paris-Diderot
Unit:
UMR-S 973
[field_pole_regional_de_rattachem]
Website
RPBS
Scientific leader(s)
Technical leader(s)
Certificat(s)
  • Label IBiSA
Infrastructure
Propriétaire
Effective storage
70.00 To
Cluster: cores number
960 cores
Data collections number
2
CPU/hours a year
913 000 H / an
Bioinformatic tools number
32
Users number (last year)
41
Servers description
  • Salle serveur de 40m²
  • Architecture de type PAAS (Platform As A Service)
  • Ferme de calcul hétérogène (noeuds 12 coeurs / 48Go de RAM, noeud 60 coeurs / 512 Go de RAM, noeud GPU en cours d'installation) sur un réseau interne 10Gb
  • Espace disque de travail de 30To sous LustreFS
  • Espace de stockage NFS de 2x30To
  • Gestion logicielle avec SaltStack
  • Encapsulation des services dans des conteneurs Docker
  • Gestionnaire de tâches: Slurm

Access conditions
  • Accès libre via le portail Mobyle
  • Accès en tant qu'utilisateur enregistré via le portail Mobyle
  • Accès direct à la ressource sur demande
  • Hébergement de matériel propriétaire en mode PAAS
Annual visits:
130 an
Unique visits:
130 an
Quotes:
4
Latest update:
Not documented

BactPepDB

Description

BactPepDB is a database of predicted peptides from an exhaustive survey of complete prokaryote genomes. It provides insights about candidate peptides, and provides information about their conservation, together with some of their expected biological/structural features. The BactPepDB interface allows to search for candidate peptides in the database, or to search for peptides similar to a query, according to the multiple properties predicted or related to genomic localization.

Access conditions
  • Service en ligne en accès libre.
  • Possibilité d'analyse spécifique sur demande.
Annual visits:
1 791 an
Unique visits:
1 433 an
Quotes:
25
Latest update:
Not documented

SPROUTS

Description

SPROUTS has been designed to give scientists access to data related to protein folding prediction. In this scope, we processed a set of proteins on five different tools devoted to the prediction of stability changes upon point mutation. We also propose the results obtained with two methods devoted for one to the direct prediction of residues involved in the core of a protein structure and for the other, the characterization of fragments which ends are assumed to be part of the folding nucleus.

Access conditions

Service en ligne en accès libre.

Annual visits:
140 an
Unique visits:
60 an
Quotes:
2
Downloads:
Not documented

BCSearch

Description

BCSearch is a fast and flexible approach to identify linear fragments similar to a query in large collections of structures. It addresses two basic questions:

  • Among a subset of structures, what sequences are compatible with the conformation of my query ?
  • Are there conformations similar to my query in other proteins ? Is it observed elsewhere ?

BCSearch is based on a new similarity approach, based on a Binet Cauchy (BC) kernel. The approach measures the correlation between the volumes of all the tetraedron of the query and that of a target. The similarity (BCscore) is scored between -1 and 1, where a value of 1 corresponds to the exact same conformation than the query, and -1 to the mirror conformation. Values close to 0 correspond to unrelated fragments. The BCscore is more stringent than other criteria such as the alpha carbon RMS deviation. Particularly, fragments with partly dissimilar shapes are poorly scored and consequently collections of matches are usually less noisy, which makes them better suited for the analysis of the local structure-sequence relationship. In addition, since no superimposition is required, the similarity search is very fast, making possible to mine large collections of structures.

Access conditions

Service en ligne en accès libre.

Annual visits:
2 470 an
Unique visits:
960 an
Quotes:
345
Downloads:
Not documented

fpocket

Description

Service en ligne libre d'accès.

Access conditions

Service en ligne en accès libre.

Annual visits:
6 400 an
Unique visits:
960 an
Quotes:
64
Downloads:
Not documented

Frog2

Description

Frog is intended to generate 3D for drugs, usually described using a 1D or 2D representation. Frog performs isomer identification from ambiguous compound description. Frog is able to generate multi-conformations per isomer.

Access conditions

Service en ligne en accès libre.

No website documented
Annual visits:
10 000 an
Unique visits:
3 200 an
Quotes:
Not documented
Downloads:
Not documented

HCA

Description

Hydrophobic cluster analysis.

Access conditions

Service en ligne en accès libre.

Annual visits:
260 an
Unique visits:
70 an
Quotes:
2
Downloads:
Not documented

HHalign-Kbest

Description

HHalign-Kbest is useful to automatically obtain optimized alignments and models in case of low sequence identity (<35%) between a query and a template protein. It can generate k suboptimal (e.g. top-k scoring) alignments rather than only the optimal one which may contain small to large errors.

Access conditions

Service en ligne en accès libre.

Annual visits:
1 120 an
Unique visits:
310 an
Quotes:
4
Downloads:
Not documented

InterEvDock2

Description

InterEvDock is a server for protein docking running the InterEvScore potential specifically designed to integrate evolutionary information in the docking process. The InterEvScore potential was developed for heteromeric protein interfaces and combines a residue-based multi-body statistical potential with evolutionary information derived from the multiple sequence alignments of each partner in the complex.

Access conditions

Service en ligne en accès libre.

Annual visits:
5 100 an
Unique visits:
1 000 an
Quotes:
14
Downloads:
Not documented

MTiAutoDock/MTiOpenScreen

Description

MTiAutoDock and MTiOpenScreen are two services dedicated to small molecule docking and chemical library virtual screening.

Access conditions

Service en ligne en accès libre.

Annual visits:
30 000 an
Unique visits:
3 900 an
Quotes:
377
Downloads:
Not documented

PEP-FOLD

Description

PEP-FOLD is a de novo approach aimed at predicting peptide structures from amino acid sequences.

This method, based on structural alphabet SA letters to describe the conformations of four consecutive residues, couples the predicted series of SA letters to a greedy algorithm and a coarse-grained force field.

Access conditions

Service en ligne en accès libre.

No website documented
Annual visits:
1 482 an
Unique visits:
347 an
Quotes:
1
Downloads:
Not documented

PEP-SiteFinder

Description

PEP-SiteFinder is a service aimed at identifying patches on a protein surface, which a peptide of specified sequence is likely to interact with.

Access conditions

Service en ligne en accès libre.

No website documented
Annual visits:
340 an
Unique visits:
26 an
Quotes:
Not documented
Downloads:
Not documented

SA-Frag

Description

SA-Frag is a service that will, given an amino acid sequence, return 3D fragments predicted to match the various positions of the sequence. SA-Frag will thus return an alignement of the fragments identified with the query and a collection of 3D structures corresponding to the fragments in the PDB format.

Access conditions

Service en ligne en accès libre.

Annual visits:
640 an
Unique visits:
130 an
Quotes:
67
Downloads:
Not documented

SABBAC

Description

SABBAC is an on-line service devoted to protein backbone reconstruction from alpha-carbon trace. It is based on the assembly of fragments issued from library of reduced size, resulting from the encoding of the protein trace in an HMM-derived structural alphabet.

Access conditions

Service en ligne en accès libre.

Annual visits:
310 an
Unique visits:
170 an
Quotes:
11
Downloads:
Not documented

wwLig-CSRre

Description

wwLigCSRre is intended for searching banks for compounds similar to a query, based on both coordinates and physico-chemical properties of atoms.

Access conditions

Service en ligne en accès libre.

Domains of activity
  • Biology
  • Computer Science
  • Biomedical
Description of expertise domains

Bioinformatique Structurale : analyse et modélisation de la structure et de la fonction des protéines, des peptides. Complexes protéiques, peptide-protéine. Criblage in silico.

  • Modélisation comparative de la structure des protéines
  • Recherche de similitudes structurales
  • Modélisation de la structure de complexes protéiques
  • Modélisation de novo de la structure des peptides
  • Criblage in silico (structure-based)
  • Impact structural de mutations ponctuelles
Keywords:
  • Bioinformatique structurale
  • Analyse des structures, recherche d'homologues et de motifs structuraux
  • Prédictions des propriétés structurales
  • Modélisation comparative et de novo de structures
  • Modélisation des interactions protéines/protéines, protéines/peptides et protéines/acides nucléiques
  • Analyse des propriétés dynamiques et thermodynamiques des structures
  • Criblage virtuel
  • Librairies de petits composés chimiques, 2D/3D, ADME/tox
  • Criblage basé sur la structure

Formation professionnelle

No website documented
Trainees:
15 trainees / year
Training time:
1 day(s) / year
No upcoming session scheduled

Python avancé

Description
Not documented
Access conditions
Not documented
Trainees:
15 trainees / year
Training time:
1 day(s) / year
No upcoming session scheduled

Introduction au portail MOBYLE

Description
Not documented
Access conditions
Not documented

Formation universitaire

No website documented
Trainees:
15 trainees / year
Training time:
1 day(s) / year
No upcoming session scheduled

Criblage de petits composés

Description
Not documented
Access conditions
Not documented
Internal publications

Lamiable A, Thévenet P, Rey J, Vavrusa M, Derreumaux P, Tufféry P.
PEP-FOLD3: faster de novo structure prediction for linear peptides in solution and in complex.
Nucleic Acids Res. 2016 Jul 8;44(W1):W449-54.


Guyon F, Martz F, Vavruša M, Bécot J, Rey J, Tufféry P.
BCSearch: fast structural fragment mining over large collections of protein structures.
Nucleic Acids Res. 2015 Jul 1;43(W1):W378-82.


Saladin A, Rey J, Thevenet P, Zacharias M, Moroy G, Tufféry P.
PEP-SiteFinder: a tool for the blind indentification of peptide binding sites on protein surfaces.
Nucleic Acids Res. 2014 Jul;42(Web Server issue):W221-6.


Shen Y, Maupetit J, Derreumaux P, Tufféry P.
Improved PEP-FOLD approach for peptide and miniprotein structure prediction
J. Chem. Theor. Comput. 2014; 10:4745-4758


Rey J, Deschavanne P, Tufféry P.
BactPepDB: a database of predicted peptides from an exhaustive survey of complete prokaryote genomes.
Database (Oxford). 2014 Nov 6;2014. pii: bau106. doi: 10.1093/database/bau106. Print 2014.


Thévenet P, Shen Y, Maupetit J, Guyon F, Derreumaux P, Tufféry P.
PEP-FOLD: an updated de novo structure prediction server for both linear and disulfide bonded cyclic peptides.
Nucleic Acids Res. 2012 Jul;40(Web Server issue):W288-93.


Shen Y, Picord G, Guyon F, Tufféry P.
Detecting protein candidate fragments using a structural alphabet profile comparison approach.
PLoS One. 2013 Nov 26;8(11)

External publications

Yu J, Picord G, Tufféry P, Guerois R.
HHalign-KBest: exploring sub-optimal alignments for remote homology comparative modeling
Bioinformatics. 2015 Dec 1;31(23):3850-2.


Yu J, Vavrusa M, Andreani J, Rey J, Tufféry P, Guerois R.
InterEvDock: A docking server to predict the structure of protein-protein interactions using evolutionary information.
Nucleic Acids Res. 2016 Jul 8;44(W1):W542-9.


Schmidtke P, Le Guilloux V, Maupetit J, Tufféry P.
fpocket: online tools for protein ensemble pocket detection and tracking.
Nucleic Acids Res. 2010 Jul;38(Web Server issue):W582-9.


Acuña R, Lacroix Z, Papandreou N, Chomilier J.
Protein intrachain contact prediction with most interacting residues (MIR).
Bio-Algorithms and Med-Systems 2014 Nov 27;10(4):227-242


Lonquety M, Lacroix Z, Papandreou N, and Chomilier J. 
SPROUTS: a database for the evaluation of protein stability upon point mutation.
Nucleic Acids Res. 2009 Jan;37(Database issue):D374-9.

Publications with the hosting laboratory

Labbé C, Rey J, Lagorce D, Vavruša M, Becot J, Sperandio O, Villoutreix B, Tufféry P, Miteva M.
MTiOpenScreen: a web server for structure-based virtual screening.
Nucleic Acids Res. 2015 Jul 1;43(W1):W448-54.


Lagorce D, Sperandio O, Baell JB, Miteva MA, Villoutreix BO.
FAF-Drugs3: a web server for compound property calculation and chemical library design.
Nucleic Acids Res. 2015 Jul 1;43(W1):W200-7.


Miteva MA, Guyon F, Tufféry P.
Frog2: Efficient 3D conformation ensemble generator for small compounds.
Nucleic Acids Res. 2010 Jul;38(Web Server issue):W622-7.

Development

PEP-FOLD (APP)

Users distribution
International
81 %
National
14 %
Regional
3 %
Local
2%
Explanation about this distribution:

La répartition présentée est celle de l'accès au portail Mobyle et donc aux accès via le Web.

Platform's own projects

Mobyle (2006-2014) :  environnement de déploiement et d'execution automatisés sur le Web

MobyleNet (2009-2011) : réseau de portails Web

Collaborations
National projets

IA Bioinformatique BipBip (Biology in processors Bayesian inference paradigm)

International and European projects
Not documented
Projects with industry
Not documented
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 ... )

Coordination du workpackage Bioinformatique Structurale du projet IFB

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