RPBS

Adress
35 rue Hélène Brion 75013 Paris
Structure(s)
INSERM, Université Paris-Diderot
Unit:
UMR-S 973
Regional Center
ApliBio, Ile-de-France
Website
RPBS
Scientific leader
Tufféry Pierre
Technical leader
Rey Julien
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
  • 40m² server room
  • PAAS architecture (Platform As A Service)
  • Heterogeneous computer cluster (12 CPU / 48GB RAM nodes, 60 CPU / 512GB RAM node, GPU node (setup in progress)
  • 30TB of working storage under LustreFS
  • 2x 30TB of data storage (NFS)
  • Configuration management with SaltStack
  • Software encapsulation with Docker
  • Ressource manager: Slurm

Access conditions
  • Free access through the Mobyle portal
  • Access as a registered user through the Mobyle portal
  • Direct on-demand access to the computational ressource
  • Proprietary hardware hosting (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

Free access

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

Online free access

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

Online free access

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

Online free access

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

Online free access

No website documented
Annual visits:
8 400 an
Unique visits:
780 an
Quotes:
35
Downloads:
Not documented

FAF-Drug2

Description

FAF-Drugs (Free ADME-Tox Filtering Tool version 3.0) is a program for filtering large compound libraries prior to in silico screening experiments or related modeling studies. The main goal is the computational prediction of some ADME-Tox properties (Adsorption, Distribution, Metabolism, Excretion and Toxicity) in order to assist hit selection before chemical synthesis or ordering.

FAF-Drugs employs pre-defined filters, but users can also customize their own filtering parameters by using the Filter-Editor service.

Access conditions

Online free access

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

Online free access

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

InterEvDock

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

Online free access

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

fpocket

Description

fpocket is a very fast, open source protein pocket (cavity) detection algorithm based on Voronoi tessellation. It was developed in the C programming language and is currently available as command line driven program, and from now as a web server too.

Access conditions

Online free access.

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

Online free access

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

Online free access

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

Online free access

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

Online free access

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

Online free access

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

Structural Bioinformatics: protein and peptide structure and function analysis, modeling. Protein-peptide complexes. In silico screening.

Non exhaustively:

  • Protein structure comparative modeling
  • Structural similarity search
  • Protein complex structure modeling
  • Peptide structure de novo modeling
  • Structure based in silico screening
  • Point mutation structural impact
Keywords:
  • Structural bioinformatics
  • Structure analysis, homologous and structural motifs discovery
  • Structural property prediction
  • Structure comparative and de novo modelling
  • Modelling of proteins/proteins, proteins/peptides and proteines/nucleic acids interactions
  • Analysis of dynamics and thermodynamics properties of structures
  • Virtual screening
  • Small chemical compounds libraries, 2D/3D, ADME/tox
  • Structure-based screening

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

Mobyle portal logs analysis.

Platform's own projects

Mobyle (2006-2014): automatic deployment and execution environment on the Web

MobyleNet (2009-2011): Web portal network

Collaborations
National projets

IA Bioinformatics 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 ... )

Structural Bioinformatics workpackage coordination (IFB project).

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)

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