RPBS
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Adress
35 rue Hélène Brion 75013 Paris
Structure(s)
INSERM, Université Paris-Diderot
Unit:
UMR-S 973
Website
RPBSScientific 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
- 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
BactPepDBDescriptionBactPepDB 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
|
Annual visits: 1 791 an
Unique visits: 1 433 an
Quotes: 25
Latest update: Not documented
SPROUTSDescriptionSPROUTS 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 conditionsFree access |
BCSearchDescriptionBCSearch is a fast and flexible approach to identify linear fragments similar to a query in large collections of structures. It addresses two basic questions:
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 conditionsOnline free access |
Annual visits: 2 470 an
Unique visits: 960 an
Quotes: 345
Downloads: Not documented
fpocketDescriptionfpocket 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 conditionsOnline free access. |
Annual visits: 6 400 an
Unique visits: 960 an
Quotes: 64
Downloads: Not documented
Frog2DescriptionFrog 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 conditionsOnline free access |
No website documentedAnnual visits: 10 000 an
Unique visits: 3 200 an
Quotes: Not documented
Downloads: Not documented
HCADescriptionHydrophobic Cluster Analysis Access conditionsOnline free access |
HHalign-KbestDescriptionHHalign-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 conditionsOnline free access |
InterEvDock2DescriptionInterEvDock 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 conditionsOnline free access |
Annual visits: 5 100 an
Unique visits: 1 000 an
Quotes: 14
Downloads: Not documented
MTiAutoDock/MTiOpenScreenDescriptionMTiAutoDock and MTiOpenScreen are two services dedicated to small molecule docking and chemical library virtual screening. Access conditionsOnline free access |
Annual visits: 30 000 an
Unique visits: 3 900 an
Quotes: 377
Downloads: Not documented
PEP-FOLDDescriptionPEP-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 conditionsOnline free access |
No website documentedAnnual visits: 1 482 an
Unique visits: 347 an
Quotes: 1
Downloads: Not documented
PEP-SiteFinderDescriptionPEP-SiteFinder is a service aimed at identifying patches on a protein surface, which a peptide of specified sequence is likely to interact with. Access conditionsOnline free access |
No website documentedAnnual visits: 340 an
Unique visits: 26 an
Quotes: Not documented
Downloads: Not documented
SA-FragDescriptionSA-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 conditionsOnline free access |
SABBACDescriptionSABBAC 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 conditionsOnline free access |
wwLig-CSRreDescriptionwwLigCSRre is intended for searching banks for compounds similar to a query, based on both coordinates and physico-chemical properties of atoms. Access conditionsOnline 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 documentedTrainees: 15 trainees / year
Training time: 1 day(s) / year
No upcoming session scheduled
Python avancéDescriptionNot documentedAccess conditionsNot documented |
No website documentedTrainees: 15 trainees / year
Training time: 1 day(s) / year
No upcoming session scheduled
Criblage de petits composésDescriptionNot documentedAccess conditionsNot documented |
Trainees: 15 trainees / year
Training time: 1 day(s) / year
No upcoming session scheduled
Introduction au portail MOBYLEDescriptionNot documentedAccess conditionsNot 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:
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
Projects with industry
Collaboration projects not founded through an external organism
Provision of services not founded through an external organism
Not documented
Animations (Workshops, Work-groups, seminars, conferences ... )
Structural Bioinformatics workpackage coordination (IFB project).
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