Protein Engineering
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
One‐shot Optimization of Multiple Enzyme Parameters: Tailoring Glucose Oxidase for pH and Electron Mediators
Published: September 14, 2019
Journal: Biotechnology & Bioengineering
A machine learning approach for reliable prediction of amino acid interactions and its application in the directed evolution of enantioselective enzymes
Published: November 13, 2018
Journal: Scientific Reports
Application of Fourier transform and proteochemometrics principles to protein engineering
Published: October 16, 2018
Authors: Frédéric Cadet, Nicolas Fontaine, Iyanar Vetrivel, Matthieu Ng Fuk Chong, Olivier Savriama, Xavier Cadet, Philippe Charton
Journal: BMC Bioinformatics
Protein Science
Versatile Dimerisation Process of Translocator Protein (TSPO) Revealed by an Extensive Sampling Based on a Coarse-Grained Dynamics Study
Published: July 22, 2020
Journal: Journal of Chemical Information and Modeling
Structural variations within proteins can be as large as variations observed across their homologues
Published: September 24, 2019
Journal: Biochimie
Non-Linear Dynamics Analysis of Protein Sequences. Application to CYP450
Published: August 31, 2019
Authors: Xavier F. Cadet, Reda Dehak, Sang Peter Chin, Miloud Bessafi
Journal: Entropy
Knowledge-based prediction of protein backbone conformation using a structural alphabet
Published: November 21, 2017
Authors: Iyanar Vetrivel, Swapnil Mahajan, Manoj Tyagi, Lionel Hoffmann, Yves-Henri Sanejouand, Narayanaswamy Srinivasan, Alexandre G. de Brevern, Frédéric Cadet, Bernard Offmann
Journal: PLoS One
Use of a structural alphabet to find compatible folds for amino acid sequences
Published: October 25, 2014
Authors: Swapnil Mahajan, Alexandre G. de Brevern, Yves-Henri Sanejouand, Narayanaswamy Srinivasan, Bernard Offmann
Journal: Protein Science
Analysis of loop boundaries using different local structure assignment methods
Published: July 15, 2009
Authors: Manoj Tyagi, Aurélie Bornot, Bernard Offmann, Alexandre G. de Brevern
Journal: Protein Science
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
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
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
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
Physico-chemical characterization
Use of Machine learning and infrared spectra for rheological characterization and application to the apricot
Published: December 16, 2019
Authors: Xavier F. Cadet, Ophélie Lo-Thong, Sylvie Bureau, Reda Dehak, Miloud Bessafi
Journal: Scientific Reports
PEACCEL’s founders publications
A glance into the evolution of template-free protein structure prediction methodologies
Published: May 15, 2020
Authors: Surbhi Dhingra, Ramanathan Sowdhamini, Frédéric Cadet, Bernard Offmann
Journal: Biochimie
Converting bulk sugars into prebiotics: semi-rational design of a transglucosylase with controlled selectivity
Published: February 3, 2016
Authors: Tom Verhaeghe, Karel De Winter, Magali Berland, Rob De Vreese, Matthias D’hooghe, Bernard Offmann, Tom Desmet
Journal: Chemical Communications
DoSA: Database of Structural Alignments
Published: July 11, 2013
Authors: Swapnil Mahajan, Garima Agarwal, Mohammed Iftekhar, Bernard Offmann, Alexandre G. de Brevern, Narayanaswamy Srinivasan
Journal: Journal of Biomolecular Structure and Dynamics
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
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
Native and modeled disulfide bonds in proteins: Knowledge-based approaches toward structure prediction of disulfide-rich polypeptides
Published: January 11, 2005
Authors: Ratna Rajesh Thangudu, Arunachalam Vinayagam, Ganesan Pugalenthi, Arunachalam Manonmani, Bernard Offmann, Ramanathan Sowdhamini
Journal: Proteins: Structure, Function, and Bioinformatics