Publications

Protein Engineering

Machine Learning Enables Selection of Epistatic Enzyme Mutants for Stability Against Unfolding and Detrimental Aggregation

Novel Descriptors and Digital Signal Processing- Based Method for Protein Sequence Activity Relationship

Published: November 11, 2019

Authors: Nicolas T. Fontaine, Xavier F. Cadet, Iyanar Vetrivel

Journal: International Journal of Molecular Sciences

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One‐shot Optimization of Multiple Enzyme Parameters: Tailoring Glucose Oxidase for pH and Electron Mediators

A machine learning approach for reliable prediction of amino acid interactions and its application in the directed evolution of enantioselective enzymes

Application of Fourier transform and proteochemometrics principles to protein engineering

Published: October 16, 2018

Authors: Frédéric Cadet, Nicolas FontaineIyanar VetrivelMatthieu Ng Fuk ChongOlivier SavriamaXavier Cadet, Philippe Charton

Journal: BMC Bioinformatics

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Protein Science

Versatile Dimerisation Process of Translocator Protein (TSPO) Revealed by an Extensive Sampling Based on a Coarse-Grained Dynamics Study

Structural variations within proteins can be as large as variations observed across their homologues

Non-Linear Dynamics Analysis of Protein Sequences. Application to CYP450

Use of a structural alphabet to find compatible folds for amino acid sequences

Analysis of loop boundaries using different local structure assignment methods

Protein short loop prediction in terms of a structural alphabet

Published: June 25, 2009

Authors: Manoj Tyagi, Aurélie Bornot, Bernard Offmann, Alexandre G. de Brevern

Journal: Computational Biology and Chemistry

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Synthetic Biology

Identification of flux checkpoints in a metabolic pathway through white-box, grey-box and black-box modeling approaches

Published: August 10, 2020

Authors: Ophélie Lo-Thong, Philippe Charton, Xavier F. Cadet, Brigitte Grondin-Perez, Emma Saavedra, Cédric Damour, Frédéric Cadet

Journal: Scientific Reports

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A Machine Learning Approach for Efficient Selection of Enzyme Concentrations and Its Application for Flux Optimization

Flux prediction using artificial neural network (ANN) for the upper part of glycolysis

Modeling of a Cell-Free Synthetic System for Biohydrogen Production

Published: March 30, 2015

Authors: Nicolas Fontaine, Brigitte Grondin-Perez, Frederic Cadet, Bernard Offmann 

Journal: Journal of Computer Science & Systems Biology

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Antibodies

Discrete analysis of camelid variable domains: sequences, structures, and in-silico structure prediction

Published: March 6, 2020

Authors: Akhila Melarkode Vattekatte, Nicolas Ken Shinada, Tarun J. Narwani, Floriane Noël, Olivier Bertrand, Jean-Philippe Meyniel, Alain Malpertuy, Jean-Christophe Gelly, Frédéric Cadet, Alexandre G. de Brevern

Journal: PeerJ

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Physico-chemical characterization

Use of Machine learning and infrared spectra for rheological characterization and application to the apricot

 

PEACCEL’s founders publications

A glance into the evolution of template-free protein structure prediction methodologies

Converting bulk sugars into prebiotics: semi-rational design of a transglucosylase with controlled selectivity

DoSA: Database of Structural Alignments

Correlation between local structural dynamics of proteins inferred from NMR ensembles and evolutionary dynamics of homologues of known structure

Published: June 3, 2013

Authors: Swapnil Mahajan, Alexandre G. de Brevern, Bernard Offmann, Narayanaswamy Srinivasan

Journal: Journal of Biomolecular Structure and Dynamics

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A substitution matrix for structural alphabet based on structural alignment of homologous proteins and its applications

Published: August 7, 2006

Authors: Manoj Tyagi, Venkataraman S. Gowri, Narayanaswamy Srinivasan, Alexandre G. de Brevern, Bernard Offmann

Journal: Proteins: Structure, Function, and Bioinformatics

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Native and modeled disulfide bonds in proteins: Knowledge-based approaches toward structure prediction of disulfide-rich polypeptides