RPBS

Address

35 rue Hélène Brion
48.827664, 2.380355

Attachment

Structure
Unit

Outlinks

homepage: [long name is missing in model]
legacy catalog: Try opening in it

Scientific Leaders

Chevrollier Nicolas

Technical Leaders

Murail Samuel
Rey Julien

Certificats

Label IBiSA

Team

Chevrollier Nicolas
Murail Samuel
Chomilier Jacques
Rey Julien
Stratmann Dirk
Tufféry Pierre
Yu Jinchao

Data

Fpocket

biotoolsID: fpocket
homepage: https://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::fpocket
last_update: Nov. 24, 2024, 8:59 p.m.
more: ...

Description

Web server which detects small molecule pockets by relying on the geometric alpha sphere theory. It also tracks pockets during molecular dynamics so to provide insight on pocket dynamics (mdpocket) and transposes mdpocket to the combined analysis of homologous structures (hpocket).

Frog

biotoolsID: frog2
homepage: https://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::Frog2
last_update: Nov. 25, 2024, 2 p.m.
more: ...

Description

Frog2 (Free Online Drug Conformation 2) is a service aimed at generating 3D conformations for small molecules starting from their 1D, 2D or 3D descriptions (smiles, sdf or mol2 input formats). Frog2 improves upon Frog1 by embedding new energy minimization and ring generation capacities.

HCA (hydrophobic cluster analysis)

biotoolsID: hca
homepage: http://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py?form=HCA#forms::HCA
last_update: Nov. 24, 2024, 3:47 p.m.
more: ...

Description

The HCA method is based on the use of a bidimensional plot, called the HCA plot. The bidimensional plot is associated with an alpha helicoidal pitch (3.6 residue/turn, connectivity distance of 4) which has been shown to offer the best correspondence between clusters and regular secondary structures. Examination of the HCA plot of a protein sequence allow to easily identify globular regions from non globular ones and, in globular regions, to identify secondary structures.

HHalign-Kbest

biotoolsID: hhalign-kbest
homepage: http://bioserv.rpbs.univ-paris-diderot.fr/services/HHalign-Kbest/
last_update: Nov. 25, 2024, 2 p.m.
more: ...

Description

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.

InterEvDock

biotoolsID: interevdock2
homepage: https://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::InterEvDock2
last_update: Nov. 24, 2024, 9 p.m.
more: ...

Description

Ab initio protein docking based on rigid-body sampling followed by consensus scoring using physics-based and statistical potentials, including the InterEvScore function specifically developed to incorporate co-evolutionary information in docking.

PEP-FOLD

biotoolsID: pep-fold
homepage: https://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::PEP-FOLD3
last_update: Nov. 24, 2024, 8:59 p.m.
more: ...

Description

PEP-FOLD uses a hidden Markov model-derived structural alphabet for de novo modeling of 3D conformations of peptides between 9-25 amino acids in aqueous solution. Updates to PEP-FOLD allow for modeling of linear and disulphide bonded cyclic peptides with 9-36 amino acids using benchmarked peptides.

PEP-SiteFinder

biotoolsID: pep-sitefinder
homepage: https://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::PEP-SiteFinder
last_update: Nov. 24, 2024, 8:59 p.m.
more: ...

Description

PEP-SiteFinder is a web server tool for the blind identification of peptide binding sites on protein surfaces.

SABBAC

biotoolsID: sabbac
homepage: https://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::SABBAC
last_update: Nov. 24, 2024, 9 p.m.
more: ...

Description

Tool for the reconstruction of complete protein structures from their alpha-carbon descriptions.

Domains of activity

Biologie
Biomédical
Informatique

Description of expertise domains

RPBS est une plateforme dédiée à la bio-informatique structurelle. Elle propose : le développement de méthodes/protocoles de bio-informatique structurelle, l'hébergement de services et le déploiement en ligne de services du domaine, la formation et conseil dans le domaine et l’hébergement de calculs via PAAS.

Keywords

Comparative and de novo structure modeling
Dynamic and thermodynamic structure properties analysis
Virtual screening
Structure-based screening
2D/3D
ADME/tox
Small chemical compound libraries
Protein/protein interaction modelisation
proteins/peptides and proteins/nucleic acids
Structure analysis
homology and structural pattern matching
Structural Bioinformatics
Predictions of structural properties

None None. None, None.

ouverture_pf.csv is not loaded in the system