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Outils bioinformatiques
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Protein Analysis Toolkit for integrated biocomputing on the web.
Jerome Gracy and Laurent Chiche (2005), Nucleic Acids ResearchWeb Server issue, 33, W65-71.Additional Sponsors: ACI-IMPBio
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Bioinformatics Tools Server, a pipeline for comparative modeling of protein-ligand complexes.
Pons JL & Labesse G.(2009) Nucleic Acids Research ; doi : 10.1093/nar/gkp368Additional Sponsors : ACI-IMPBio
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A tool for incremental threading optimization in order to help alignment and molecular modeling at any sequence similarity level.
Labesse G. and Mornon JP, (1998) Bioinformatics14, 206-211 -
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.
Catherinot, V and Labesse, G.(2004) Bioinformatics20,3694-3696Additional Sponsors : Inserm (AIGE)
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A program for secondary structure assignment from Ca
Labesse G., Colloc'h N., Pothier J. and Mornon J.-P., (1997)
CABIOS vol 13., no. 3, pages 291-295 -
EvDTree creates structure-dependent substitution profiles based on decision tree classification of 3D environments.
Gelly, J.-C., Chiche, L. and Gracy, J. (2005), BMC Bioinformatics 6:4Additional Sponsors : Action, Bioinformatique, Inter-EPST
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A Ligand Transposition Server : This server allows comparative docking of ligands into the ATP-binding site of a protein kinase (target)
Martin L, Catherinot V, Labesse G.(2006) Nucleic Acids Research Web Server issue:34 W325-W329Additional Sponsors : La Ligue contre le cancer
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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.
Benod C., Delsuc MA., Pons JL (2006) J. Chem. Inf. Model. 46 (3) 1517-1522Additional Sponsors : ACI-IMPBio
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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 determinationDumas C. & van der Lee A. (2008) "Macromolecular structure solution by charge flipping", Acta Cryst D64, 864-873.
Palatinus L. & Chapuis G. (2007) "SUPERFLIP, a computer program for the solution of crystal structures by charge flipping in arbitrary dimensions", J. Appl. Cryst.40,786-790.
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This web server is dedicated to the protein structural family of Knottins
Gelly JC, Gracy J, Kaas Q, Le-Nguyen D, Heitz A, Chiche L. (2004) Nucleic Acids Res.;32(1):D156-9.
Postic G, Gracy J, Périn C, Chiche L, Gelly JC. (2018) Nucleic Acids Res.;46(D1):D454-D8.Additional Sponsors : ACI-IMPBio
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A protein-protein complex structure by SAXS and computational docking
B Jiménez-García, C Pons, DI. Svergun, P Bernadó and J Fernández-Recio.
Nucleic Acids Research 2015; doi: 10.1093/nar/gkv368 -
Calculation of sequence specific protein solvent accessibilities in the unfolded ensemble
Estrada, J., Bernadó, P., Blackledge, M., and Sancho, J. (2009). ProtSA: a web application for calculating sequence specific protein solvent accessibilities in the unfolded ensemble. BMC Bioinformatics, 10, 104. URL
Bernadó, P., Blackledge, M., and Sancho, J. (2006). Sequence-specific solvent accessibilities of protein residues in unfolded protein ensembles. Biophysical Journal, 91, 4536–4543. URL -
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Automatic detection of diffusion modes within biological membranes using backpropagation neural network
Dosset P., Rassam P., Fernandez L., Espenel C., Rubinstein E., Margeat E. and Milhiet P.E. ( 2016 ) BMC Bioinformatics ( in press )
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- All
- Y Sequence Analysis
- Y Structure Modeling
- Z Ligand Interaction
-
Protein Analysis Toolkit for integrated biocomputing on the web.
Jerome Gracy and Laurent Chiche (2005), Nucleic Acids ResearchWeb Server issue, 33, W65-71.Additional Sponsors: ACI-IMPBio
-
Bioinformatics Tools Server, a pipeline for comparative modeling of protein-ligand complexes.
Pons JL & Labesse G.(2009) Nucleic Acids Research ; doi : 10.1093/nar/gkp368Additional Sponsors : ACI-IMPBio
-
A tool for incremental threading optimization in order to help alignment and molecular modeling at any sequence similarity level.
Labesse G. and Mornon JP, (1998) Bioinformatics14, 206-211 -
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.
Catherinot, V and Labesse, G.(2004) Bioinformatics20,3694-3696Additional Sponsors : Inserm (AIGE)
-
A program for secondary structure assignment from Ca
Labesse G., Colloc'h N., Pothier J. and Mornon J.-P., (1997)
CABIOS vol 13., no. 3, pages 291-295 -
EvDTree creates structure-dependent substitution profiles based on decision tree classification of 3D environments.
Gelly, J.-C., Chiche, L. and Gracy, J. (2005), BMC Bioinformatics 6:4Additional Sponsors : Action, Bioinformatique, Inter-EPST
-
An interactive online or local Java tool for homology modelling and protein family study coupling a full featured alignment editor with a complete 3D viewer.
Grand F, Pons JL, Labesse, G (2016)
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Several genomes, databases, or protein family have been modeled during various studies with the help of automatic procedure of @TOME. The generated models are accessible from this database.
Reference : Pons JL & Labesse G.(2009) Nucleic Acids Research ; doi : 10.1093/nar/gkp368
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Several genomes, databases, or protein family have been modeled during various studies with the help of automatic procedure of @TOME. The generated models are accessible from this database.
Reference : Pons JL & Labesse G.(2009) Nucleic Acids Research ; doi : 10.1093/nar/gkp368
-
This web server is dedicated to the protein structural family of Knottins
Gelly JC, Gracy J, Kaas Q, Le-Nguyen D, Heitz A, Chiche L. (2004) Nucleic Acids Res.;32(1):D156-9.
Postic G, Gracy J, Périn C, Chiche L, Gelly JC. (2018) Nucleic Acids Res.;46(D1):D454-D8.Additional Sponsors : ACI-IMPBio
-
-
An interactive online or local Java tool for homology modelling and protein family study coupling a full featured alignment editor with a complete 3D viewer.
Grand F, Pons JL, Labesse, G (2016)
