Partenaires

CNRS


Rechercher

Sur ce site

Sur le Web du CNRS


Accueil > Outils

Logiciels

Equipe de D.Rognan, Strasbourg

Nom de l’outil Mots-clés Description Langage Distribution Email
sc-PDB Site actifs Base de données de 8000 sites de liaisons droguables de la PDB Php, MySQL ftp, site web rognan@unistra.fr
Bioinfo Molécules commerciales Base de données de 3 millions de molécules commerciales drug-like Php, MySQL ftp, site web rognan@unistra.fr
FingerPrintLib Fingerprints d’interaction Génération de fingerprint d’interaction protéine-ligand pour scorer des poses de docking (nécessite le toolkit OEChem) C++ Code source + executables rognan@unistra.fr
SiteAlign sites actifs Alignement et mesure de similarité entre sites actifs de protéines C++ Code source + executables rognan@unistra.fr
FuzCav sites actifs Mesure de similarité entre sites actifs de protéines Java Code source + executables rognan@unistra.fr
Shaper sites actifs Alignement et mesure de similarité entre sites actifs de protéines (nécessite Shaper et toolkit OEShape) C++ Code source + executables rognan@unistra.fr
VolSite Détection de cavité Détection et annotation de cavités protéiques C++ Code source + executables rognan@unistra.fr

Equipe de B. Villoutreix, Paris-7

Nom de l’outil Mots-clés Langage Distribution Email
Nombreux outils chémoinformatique F77 Online petitjean.chiral@gmail.com

(Inserm U973)

FAF-Drugs2 Préparation de chimiothèques Python, C WEB, Source Code.
Server version
david.lagorce@univ-paris-diderot.fr

(Inserm U973)

PPIFocusDB Collections enrichies en inhibiteur d interaction proteine-proteine Java, python binaire olivier.sperandio@inserm.fr

(Inserm U973)

In preparation Database of protein-protein interaction inhibitors Java Online olivier.sperandio@inserm.fr

(U973)

wwLig-CSRre Ligand-based screening Online pierre.tuffery@univ-paris-diderot.fr

(Inserm U973)

ammos Small compounds minimizer C Online maria.miteva@univ-paris-diderot.fr

(Inserm U973)

DG-AMMOS Small compound single conformer 3D generation C Online maria.miteva@univ-paris-diderot.fr

(U973)

Frog and Frog2 FRee Online druG conformation generation C Online pierre.tuffery@univ-paris-diderot.fr

(U973)

MS-Dock Small compound rigid body docking and multi-conformer generator C Online : Source at the DOCK web site maria.miteva@univ-paris-diderot.fr

(U973)

fpocket Pocket prediction C Online pierre.tuffery@univ-paris-diderot.fr

(U973)

Equipe de X. Morelli, Marseille

Nom de l’outil Mots-clés Description Langage Distribution Email
2P2IDB Protein-Protein Interactions

Small molecule inhibitors

3D Structure

Structural database dedicated to protein-protein complexes and their inhibitors PhP, HTML

MySQL

Perl

Web interface morelli@ifr88.cnrs-mrs.fr, philippe.roche@ifr88.cnrs-mrs.fr
2P2ISCORE Scoring function

Druggability

PPI Drug targets

Scoring function to assess the druggability of protein-protein interactions PhP, HTML

Tcl, Perl

Web server morelli@ifr88.cnrs-mrs.fr, philippe.roche@ifr88.cnrs-mrs.fr
2P2ICHEM Targeted Chemical Library

Filtration protocol

Molecular descriptors

Filtering protocol to design focused chemical libraries dedicated to protein-protein interactions PhP, HTML

Tcl, Perl

Web server morelli@ifr88.cnrs-mrs.fr, philippe.roche@ifr88.cnrs-mrs.fr

Equipe d’A. Varnek, Strasbourg

Nom de l’outil Mots-clés Description Langage Distribution Email
ISIDA/QSPR QSAR, QSPR, ensemble modeling, fragment descriptors Obtaining and validation of QSAR/QSPR models DELPHI Binaire

Download

varnek

@unistra.fr

ISIDA/EdiSDF Chemical Database tool Chemical Database tool DELPHI Binaire

Download

varnek

@unistra.fr

ISIDA/EdChems 2D sketcher 2D sketcher DELPHI Binaire

Download

varnek

@unistra.fr

ISIDA/SQS QSAR, QSPR, ensemble modeling, FPT descriptors Obtaining and validation of QSAR/QSPR models Free Pascal Binaire horvath

@chimie

.u-strasbg.fr

ISIDA/Platform for virtual sreening Virtual screening, similarity search, QSAR models, ISIDA descriptors Virtual screening using similarity search and QSAR models based on the ISIDA descriptors Free Pascal Online horvath

@chimie

.u-strasbg.fr

ISIDA/Fragmentor Fragment descriptors, Graph algorithms, Pharmacophores, Molecular coloration Generates ISIDA Molecular Fragments Free Pascal Binaire

Download

g.marcou

@unistra.fr

ISIDA/Predictor QSA/PR models, applicability domain, XML, CGI Applies a QSAR model for any set of molecules Free Pascal Online g.marcou

@unistra.fr

ISIDA/ColorAtom QSA/PR models, interpretability, atom coloration Estimates atom contribution to a QSAR model Free Pascal Binaire g.marcou

@unistra.fr

ISIDA/Bayes Data maining, Naive Bayes, Binomial distribution Build binomial Naive Bayes models Free Pascal Binaire g.marcou

@unistra.fr

ISIDA/VP Data mining, neural networks Build a Voting Perceptron model Free Pascal Binaire g.marcou

@unistra.fr

ISIDA/ModelAnalyzerC Data mining, model estimation, classification An interactive software for analysis of performances of classification chemo-

informatics models

Free Pascal Binaire g.marcou

@unistra.fr

ISIDA/ModelAnalyzerR Data mining, model estimation, regression An interactive software for analysis of performances of regression chemo-

informatics models

Free Pascal Binaire g.marcou

@unistra.fr

ISIDA/SOMView Data mining, SOM An interactive software for analysis of SOM of chemicals Free Pascal Binaire g.marcou

@unistra.fr

ISIDA/CrossValidate Data mining, validation Split and SDF database in training and test sets according to cross-validation, bootstrapping and scrambling Free Pascal Binaire g.marcou

@unistra.fr

ISIDA/Kernel Data mining, kernel, graph, factor analysis Uses the kernel trick to perform graph representation of database, kernel PCA and kernel Factor Analysis Free Pascal Binaire g.marcou

@unistra.fr

Equipe de G. Labesse, Montpellier

Nom de l’outil Mots-clés Description Distribution Email
PAT Protein, sequence analysis PAT : a Protein Analysis Toolkit for integrated biocomputing on the web. Online labesse@cbs.cnrs.fr
Propsearch Protein, sequence analysis Propsearch : Sequence homology using amino acid composition. (by Uwe Hobohm and Chris Sander) Online labesse@cbs.cnrs.fr
CLOE Protein, sequence analysis CLOE is a software especially devoted to the proteolysis analysis Online labesse@cbs.cnrs.fr
@TOME V2 Protein structure analysis and modeling tools, Protein-ligand interactions @TOME V2 Bioinformatics Tools Server : a pipeline for comparative modeling of protein-ligand complexes. Online labesse@cbs.cnrs.fr
TITO Protein structure analysis and modeling tools TITO : a tool for incremental threading optimization in order to help alignment and molecular modeling at any sequence similarity level. Online labesse@cbs.cnrs.fr
VITO Protein structure analysis and modeling tools VITO : an interactive tool for homology modelling and protein family study coupling a full featured alignment editor with a complete 3D viewer. ViTO has its own macro language. Online labesse@cbs.cnrs.fr
P-SEA Protein structure analysis and modeling tools P-SEA : a program for secondary structure assignment from Ca Online labesse@cbs.cnrs.fr
EvDTree Protein structure evaluation EvDTree : EvDTree creates structure-dependent substitution profiles based on decision tree classification of 3D environments. Online labesse@cbs.cnrs.fr
Eval123D Protein structure evaluation Eval123D : This server allows evaluation of 3D protein structures with different methods in a single run (Verify3D, Eval23D, Prosa II, EvTree) Online labesse@cbs.cnrs.fr
Polymer/Ligand Contact Protein-ligand interactions Polymer/Ligand Contacts Visualizer : This service allows one to visualize Polymer Chain/Ligand contacts in PDB file. (Ligand can be small molecule, sugar, nucleic acid or peptide). Online labesse@cbs.cnrs.fr
LEA3D Protein-ligand interactions LEA3D : A Computer-Aided Ligand Design for Structure-Based Drug Design Online labesse@cbs.cnrs.fr
KinDOCK Protein-ligand interactions KinDOCK : A Ligand Transposition Server : This server allows comparative docking of ligands into the ATP-binding site of a protein kinase (target) Online labesse@cbs.cnrs.fr
SimDOCK Protein-ligand interactions SimDOCK : A Ligand Transposition Server : This server allows rapid selection of ligands fitting the active site of the submitted protein by superposition of its three-dimensional structure with those of known complexes of protein/ligands of the family. Online labesse@cbs.cnrs.fr
NPK NMR data processing NPK NMR Processing Kernel, a python based NMR processing program. This is a replacement for the Gifa project, still in beta though. Fully pipeline-able Online labesse@cbs.cnrs.fr
GIFA NMR data processing GIFA : a computer program designed for the processing, the visualization and the analysis of 1D, 2D, and 3D NMR data-set Online labesse@cbs.cnrs.fr
RESCUE ( & RescueN ) NMR Assignment Toolkit RESCUE ( & RescueN ) : NMR residu typing assignment aid software based on Neural Networks Online labesse@cbs.cnrs.fr
RESCUE2 NMR Assignment Toolkit Rescue2 : program for amino acid type assignment based on a probabilistic model of NMR chemical shifts distributions. Online labesse@cbs.cnrs.fr
CRAACK NMR Assignment Toolkit CRAACK : Consensus Rules for Amino-Acid Characterisation using a Kernel method (SVM). The spin system typing consensus is based on the following softwares : Rescue, RescueN, Rescue2, Platon, and one other using SVM algorithm. Online labesse@cbs.cnrs.fr
CCSP NMR Assignment Toolkit CCSP : Consensus for Chemical Shift Prediction. (based on the following softwares : Shifty v1.4, Orb v1.2, Shifts v4.1.1, Proshifts and Shiftx). Online labesse@cbs.cnrs.fr
DExt NMR Assignment Toolkit DExt : Distance Extraction from PDB file. Online labesse@cbs.cnrs.fr
CROWD NMR Assignment Toolkit CROWD Noe intensity simulation software. (An estimate of spin diffusion in a spin subset : Application to iterative distance calculation from 3D 15N NOESY-HMQC. Online labesse@cbs.cnrs.fr
CINDY NMR Assignment Toolkit CINDY : a graphical NMR assignment software. Online labesse@cbs.cnrs.fr
NMRb Databases NMR data-sets bank : A repository for raw NMR data-sets Online labesse@cbs.cnrs.fr
Knottins Databases Knottins Web site : This web is dedicated to the protein structural family of Knottins Online labesse@cbs.cnrs.fr
DOMO Databases DOMO : This database contains a collection of aligned protein domain families. Online labesse@cbs.cnrs.fr
BOUND-BOUND Databases BOUND-BOUND is a database of protein-protein co-crystallized structures build on the basis of biological unit files from PDB. Online labesse@cbs.cnrs.fr
BIOEQS biomolecular data analysis BIOEQS BIOEQS is a data fitting software package designed for analysis of data for biomolecular interactions and conformational changes. Online labesse@cbs.cnrs.fr
SUPERFLIP Crystallographic tools Adapting the Charge Flipping algorithm to biological macromolecule diffraction data :

* ab initio determination of protein crystal structures at atomic resolution

* heavy atom or anomalous scatterers substructure determination

Online labesse@cbs.cnrs.fr
SelenoCYS Crystallographic tools A protocol for the incorporation of selenomethionine and selenocysteine into recombinant proteins overexpressed in Escherichia coli based on the use of a suitable cysteine auxotrophic strain. Online labesse@cbs.cnrs.fr