Search Results - "Tufféry, P."

A critical assessment of hidden markov model sub-optimal sampling strategies applied to the generation of peptide 3D models by Lamiable, A., Thevenet, P., Tufféry, P.

“…Hidden Markov Model derived structural alphabets are a probabilistic framework in which the complete conformational space of a peptidic chain is described in…”
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Frog: a FRee Online druG 3D conformation generator by Leite, T. Bohme, Gomes, D, Miteva, M.A, Chomilier, J, Villoutreix, B.O, Tufféry, P

“…In silico screening methods based on the 3D structures of the ligands or of the proteins have become an essential tool to facilitate the drug discovery…”
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Exploring an alignment free approach for protein classification and structural class prediction by Deschavanne, P., Tufféry, P.

“…Alignment free methods based on Chaos Game Representation (CGR), also known as sequence signature approaches, have proven of great interest for DNA sequence…”
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A Hidden Markov Model Derived Structural Alphabet for Proteins by Camproux, A.C, Gautier, R, Tufféry, P

“…Understanding and predicting protein structures depends on the complexity and the accuracy of the models used to represent them. We have set up a hidden Markov…”
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RPBS: a web resource for structural bioinformatics by Alland, C., Moreews, F., Boens, D., Carpentier, M., Chiusa, S., Lonquety, M., Renault, N., Wong, Y., Cantalloube, H., Chomilier, J., Hochez, J., Pothier, J., Villoutreix, B. O., Zagury, J.-F., Tufféry, P.

“…RPBS (Ressource Parisienne en Bioinformatique Structurale) is a resource dedicated primarily to structural bioinformatics. It is the result of a joint effort…”
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SCit: web tools for protein side chain conformation analysis by Gautier, R., Camproux, A.-C., Tufféry, P.

“…SCit is a web server providing services for protein side chain conformation analysis and side chain positioning. Specific services use the dependence of the…”
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Hidden Markov Model-derived structural alphabet for proteins: The learning of protein local shapes captures sequence specificity by Camproux, A.C., Tufféry, P.

“…Understanding and predicting protein structures depend on the complexity and the accuracy of the models used to represent them. We have recently set up a…”
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CS-PSeq-Gen: Simulating the evolution of protein sequence under constraints by TUFFERY, P

“…CS-PSeq-Gen is a program derived from PSeq-Gen, designed to perform simulations of the evolution of protein sequences under the constraints of a reconstructed…”
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A coarse-grained protein force field for folding and structure prediction by Maupetit, Julien, Tuffery, P., Derreumaux, Philippe

“…We have revisited the protein coarse‐grained optimized potential for efficient structure prediction (OPEP). The training and validation sets consist of 13 and…”
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Predicting the disulfide bonding state of cysteines using protein descriptors by Mucchielli-Giorgi, M.H., Hazout, S., Tufféry, P.

“…Knowledge of the disulfide bonding state of the cysteines of proteins is of major interest in designing numerous molecular biology experiments, or in…”
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A Hidden Markov Model applied to the protein 3D structure analysis by Regad, L., Guyon, F., Maupetit, J., Tufféry, P., Camproux, A.C.

“…Understanding and predicting protein structures depend on the complexity and the accuracy of the models used to represent them. A Hidden Markov Model has been…”
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Frog2: Efficient 3D conformation ensemble generator for small compounds by Miteva, Maria A, Guyon, Frederic, Tufféry, Pierre

“…Frog is a web tool dedicated to small compound 3D generation. Here we present the new version, Frog2, which allows the generation of conformation ensembles of…”
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Critical assessment of side-chain conformational space sampling procedures designed for quantifying the effect of side-chain environment by Gautier, R., Tufféry, P.

“…We introduce a family of procedures designed to sample side‐chain conformational space at particular locations in protein structures. These procedures (CRSP)…”
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Prediction of protein side chain conformations: a study on the influence of backbone accuracy on conformation stability in the rotamer space by Tufféry, P, Etchebest, C, Hazout, S

“…We have studied the effect of backbone inaccuracy on the efficiency of protein side chain conformation prediction using rotamer libraries. The backbones were…”
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Exploring a hybrid space minimization procedure by Tufféry, P.

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PredAcc : prediction of solvent accessibility by MUCCHIELLI-GIORGI, M. H, HAZOUT, S, TUFFERY, P

“…PredAcc is a tool for predicting the solvent accessibility of protein residues from the sequence at different relative accessibility levels (0-55%). The…”
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wwLigCSRre: a 3D ligand-based server for hit identification and optimization by Sperandio, O, Petitjean, M, Tuffery, P

“…The wwLigCSRre web server performs ligand-based screening using a 3D molecular similarity engine. Its aim is to provide an online versatile facility to assist…”
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SABBAC: online Structural Alphabet-based protein BackBone reconstruction from Alpha-Carbon trace by Maupetit, Julien, Gautier, R, Tufféry, Pierre

“…SABBAC is an on-line service devoted to protein backbone reconstruction from alpha-carbon trace. It is based on the assembly of fragments taken from a library…”
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Exploring the use of a structural alphabet for structural prediction of protein loops by Camproux, A. C., Brevern, A. G., Hazout, S., Tufféry, P.

“…The prediction of loop conformations is one of the challenging problems of homology modeling, due to the large sequence variability associated with these parts…”
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PCE: web tools to compute protein continuum electrostatics by Miteva, Maria A., Tufféry, Pierre, Villoutreix, Bruno O.

“…PCE (protein continuum electrostatics) is an online service for protein electrostatic computations presently based on the MEAD (macroscopic electrostatics with…”
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