List of works - Alexandre G de Brevern

"Pinning strategy": a novel approach for predicting the backbone structure in terms of protein blocks from sequence.

scientific article

'Protein Peeling': an approach for splitting a 3D protein structure into compact fragments.

scientific article

3D Structural Models of Transmembrane Proteins ⬇️

scientific article published on January 1, 2010

A dominant mutation in the gene encoding the erythroid transcription factor KLF1 causes a congenital dyserythropoietic anemia

scientific article

A minimum set of stable blocks for rational design of polypeptide chains

scientific article published on 19 February 2019

A new prediction strategy for long local protein structures using an original description

scientific article

A novel evaluation of residue and protein volumes by means of Laguerre tessellation

scientific article published in May 2010

A recombinant dromedary antibody fragment (VHH or nanobody) directed against human Duffy antigen receptor for chemokines

scientific article

A reduced amino acid alphabet for understanding and designing protein adaptation to mutation.

scientific article published on 13 June 2007

A short survey on protein blocks.

scientific article

A structural model of a seven-transmembrane helix receptor: the Duffy antigen/receptor for chemokine (DARC).

scientific article published in August 2005

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

scientific article published on 01 October 2006

Accurate Representation of Protein-Ligand Structural Diversity in the Protein Data Bank (PDB)

scientific article published on 24 March 2020

Alloimmunization risk associated with amino acid 223 substitution in the RhD protein: analysis in the light of molecular modeling

article

AlphaIIbbeta3 integrin: new allelic variants in Glanzmann thrombasthenia, effects on ITGA2B and ITGB3 mRNA splicing, expression, and structure-function

scientific article published in March 2010

Analysing the Structural Effect of Point Mutations of Cytotoxic Necrotizing Factor 1 (CNF1) on Lu/BCAM Adhesion Glycoprotein Association.

scientific article published on 13 March 2018

Analysis of Protein Disorder Predictions in the Light of a Protein Structural Alphabet

scientific article published on 20 July 2020

Analysis of loop boundaries using different local structure assignment methods.

scientific article published on September 2009

Analysis of protein chameleon sequence characteristics.

scientific article published on 04 May 2009

Analysis of protein contacts into Protein Units.

scientific article published on 19 April 2009

Analyzing the sequence-structure relationship of a library of local structural prototypes.

scientific article

Assignment of PolyProline II conformation and analysis of sequence--structure relationship

scientific article (publication date: 2011)

Bioinformatic analysis of the protein/DNA interface.

scientific article published on 11 December 2013

Cis-trans peptide variations in structurally similar proteins

scientific article published on 8 January 2012

Comparative Analysis of Threshold and Tessellation Methods for Determining Protein Contacts

article

Comparative analysis of missing value imputation methods to improve clustering and interpretation of microarray experiments

scientific article

Comparison of tertiary structures of proteins in protein-protein complexes with unbound forms suggests prevalence of allostery in signalling proteins.

scientific article

Computational fragment-based drug design to explore the hydrophobic sub-pocket of the mitotic kinesin Eg5 allosteric binding site

scientific article published on 17 June 2009

Computational fragment-based drug design to explore the hydrophobic subpocket of the mitotic kinesin Eg5 allosteric binding site

Conservation of structural fluctuations in homologous protein kinases and its implications on functional sites.

scientific article

Correction: Modeling and Molecular Dynamics of HPA-1a and -1b Polymorphisms: Effects on the Structure of the β3 Subunit of the αIIbβ3 Integrin

scientific article published in PLoS ONE

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

scientific article published on 3 June 2013

Dimerization and phosphorylation of Lutheran/basal cell adhesion molecule are critical for its function in cell migration on laminin

scientific article published on 14 August 2019

Enzymatic Synthesis of Galactosylated Serine/Threonine Derivatives by β-Galactosidase from Escherichia coli.

scientific article published on 15 June 2015

Evolution study of the Baeyer-Villiger monooxygenases enzyme family: functional importance of the highly conserved residues.

scientific article published on 22 March 2013

Extension of a local backbone description using a structural alphabet: a new approach to the sequence-structure relationship.

scientific article

Extension of the classical classification of β-turns

scientific article published on 15 September 2016

Fast and automated functional classification with MED-SuMo: an application on purine-binding proteins.

scientific article

From local structure to a global framework: recognition of protein folds.

scientific article published on 16 April 2014

Functional annotation strategy for protein structures.

scientific article published on 19 March 2007

Genome compartimentation by a hybrid chromosome model (HXM). Application to Saccharomyces cerevisae subtelomeres

scientific article published in July 2002

Global analysis of VHHs framework regions with a structural alphabet

scientific article published on 6 September 2016

Halogens in Protein-Ligand Binding Mechanism: A Structural Perspective

scientific article published on 28 May 2019

Identification of local conformational similarity in structurally variable regions of homologous proteins using protein blocks

scientific article

Impact of protein dynamics on secondary structure prediction

scientific article published on 15 September 2020

Improvement of protein structure comparison using a structural alphabet ⬇️

scientific article published on May 5, 2011

Improving protein fold recognition with hybrid profiles combining sequence and structure evolution.

scientific article

In silico analysis of Glanzmann variants of Calf-1 domain of αIIbβ3 integrin revealed dynamic allosteric effect.

scientific article published on 14 August 2017

In silico local structure approach: a case study on outer membrane proteins

scientific article

In silico prediction of protein flexibility with local structure approach

scientific article published on 01 August 2019

In silico studies on DARC.

scientific article

Influence of assignment on the prediction of transmembrane helices in protein structures

scientific article published on 28 March 2010

Investigating the Product Profiles and Structural Relationships of New Levansucrases with Conventional and Non-Conventional Substrates

scientific article published on 29 July 2020

Investigation of the impact of PTMs on the protein backbone conformation

scientific article published on 10 June 2019

Knowledge-based prediction of protein backbone conformation using a structural alphabet

scientific article published on 21 November 2017

Local dynamics of proteins and DNA evaluated from crystallographic B factors

scientific article

Local structural differences in homologous proteins: specificities in different SCOP classes

scientific article

Modeling and molecular dynamics of HPA-1a and -1b polymorphisms: effects on the structure of the β3 subunit of the αIIbβ3 integrin

scientific article

Modeling and molecular dynamics simulations of the V33 variant of the integrin subunit β3: Structural comparison with the L33 (HPA-1a) and P33 (HPA-1b) variants

scientific article

Molecular characterization of 13 new RHD alleles.

scientific article

Multiple interests in structural models of DARC transmembrane protein.

scientific article published on 23 July 2010

New opportunities to fight against infectious diseases and to identify pertinent drug targets with novel methodologies

scientific article published on June 2009

ORION: a web server for protein fold recognition and structure prediction using evolutionary hybrid profiles

scientific article

PRR repeats in the intracellular domain of KISS1R are important for its export to cell membrane.

scientific article

PTM-SD: a database of structurally resolved and annotated posttranslational modifications in proteins.

scientific article

PolyprOnline: polyproline helix II and secondary structure assignment database

scientific article

Predicting protein flexibility through the prediction of local structures

scientific article

Prediction of the intestinal resistome by a three-dimensional structure-based method

scientific article published on 26 November 2018

PredyFlexy: flexibility and local structure prediction from sequence.

scientific article

Progressive structure-based alignment of homologous proteins: Adopting sequence comparison strategies.

scientific article

Protein Peeling 3D: new tools for analyzing protein structures.

scientific article

Protein beta-turn assignments

scientific article

Protein contacts, inter-residue interactions and side-chain modelling.

scientific article

Protein flexibility in the light of structural alphabets

scientific article

Protein secondary structure assignment revisited: a detailed analysis of different assignment methods.

scientific article

Protein short loop prediction in terms of a structural alphabet

scientific article published on 25 June 2009

Recent advances on polyproline II.

scientific article published on 9 February 2017

Same but not alike: Structure, flexibility and energetics of domains in multi-domain proteins are influenced by the presence of other domains.

scientific article published on 12 February 2018

Sequence-structure relationship study in all-α transmembrane proteins using an unsupervised learning approach.

scientific article

Species specific amino acid sequence-protein local structure relationships: An analysis in the light of a structural alphabet.

scientific article

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

scientific article published on 24 September 2019

Studies of a murine monoclonal antibody directed against DARC: reappraisal of its specificity.

scientific article

Trends in IT Innovation to Build a Next Generation Bioinformatics Solution to Manage and Analyse Biological Big Data Produced by NGS Technologies

scientific article

Understanding the role of domain-domain linkers in the spatial orientation of domains in multi-domain proteins

scientific article

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

scientific article

VHH Structural Modelling Approaches: A Critical Review

scientific article published in 2022

VLDP web server: a powerful geometric tool for analysing protein structures in their environment.

scientific article published on 12 June 2013

iPBAvizu: a PyMOL plugin for an efficient 3D protein structure superimposition approach

scientific article published on 02 November 2019

mulPBA: an efficient multiple protein structure alignment method based on a structural alphabet.

scientific article

List of works by Alexandre G de Brevern

"Pinning strategy": a novel approach for predicting the backbone structure in terms of protein blocks from sequence.

'Protein Peeling': an approach for splitting a 3D protein structure into compact fragments.

3D Structural Models of Transmembrane Proteins ⬇️

A dominant mutation in the gene encoding the erythroid transcription factor KLF1 causes a congenital dyserythropoietic anemia

A minimum set of stable blocks for rational design of polypeptide chains

A new prediction strategy for long local protein structures using an original description

A novel evaluation of residue and protein volumes by means of Laguerre tessellation

A recombinant dromedary antibody fragment (VHH or nanobody) directed against human Duffy antigen receptor for chemokines

A reduced amino acid alphabet for understanding and designing protein adaptation to mutation.

A short survey on protein blocks.

A structural model of a seven-transmembrane helix receptor: the Duffy antigen/receptor for chemokine (DARC).

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

Accurate Representation of Protein-Ligand Structural Diversity in the Protein Data Bank (PDB)

Alloimmunization risk associated with amino acid 223 substitution in the RhD protein: analysis in the light of molecular modeling

AlphaIIbbeta3 integrin: new allelic variants in Glanzmann thrombasthenia, effects on ITGA2B and ITGB3 mRNA splicing, expression, and structure-function

Analysing the Structural Effect of Point Mutations of Cytotoxic Necrotizing Factor 1 (CNF1) on Lu/BCAM Adhesion Glycoprotein Association.

Analysis of Protein Disorder Predictions in the Light of a Protein Structural Alphabet

Analysis of loop boundaries using different local structure assignment methods.

Analysis of protein chameleon sequence characteristics.

Analysis of protein contacts into Protein Units.

Analyzing the sequence-structure relationship of a library of local structural prototypes.

Assignment of PolyProline II conformation and analysis of sequence--structure relationship

Bioinformatic analysis of the protein/DNA interface.

Cis-trans peptide variations in structurally similar proteins

Comparative Analysis of Threshold and Tessellation Methods for Determining Protein Contacts

Comparative analysis of missing value imputation methods to improve clustering and interpretation of microarray experiments

Comparison of tertiary structures of proteins in protein-protein complexes with unbound forms suggests prevalence of allostery in signalling proteins.

Computational fragment-based drug design to explore the hydrophobic sub-pocket of the mitotic kinesin Eg5 allosteric binding site

Computational fragment-based drug design to explore the hydrophobic subpocket of the mitotic kinesin Eg5 allosteric binding site

Conservation of structural fluctuations in homologous protein kinases and its implications on functional sites.

Correction: Modeling and Molecular Dynamics of HPA-1a and -1b Polymorphisms: Effects on the Structure of the β3 Subunit of the αIIbβ3 Integrin

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

Dimerization and phosphorylation of Lutheran/basal cell adhesion molecule are critical for its function in cell migration on laminin

Enzymatic Synthesis of Galactosylated Serine/Threonine Derivatives by β-Galactosidase from Escherichia coli.

Evolution study of the Baeyer-Villiger monooxygenases enzyme family: functional importance of the highly conserved residues.

Extension of a local backbone description using a structural alphabet: a new approach to the sequence-structure relationship.

Extension of the classical classification of β-turns

Fast and automated functional classification with MED-SuMo: an application on purine-binding proteins.

From local structure to a global framework: recognition of protein folds.

Functional annotation strategy for protein structures.

Genome compartimentation by a hybrid chromosome model (HXM). Application to Saccharomyces cerevisae subtelomeres

Global analysis of VHHs framework regions with a structural alphabet

Halogens in Protein-Ligand Binding Mechanism: A Structural Perspective

Identification of local conformational similarity in structurally variable regions of homologous proteins using protein blocks

Impact of protein dynamics on secondary structure prediction

Improvement of protein structure comparison using a structural alphabet ⬇️

Improving protein fold recognition with hybrid profiles combining sequence and structure evolution.

In silico analysis of Glanzmann variants of Calf-1 domain of αIIbβ3 integrin revealed dynamic allosteric effect.

In silico local structure approach: a case study on outer membrane proteins

In silico prediction of protein flexibility with local structure approach

In silico studies on DARC.

Influence of assignment on the prediction of transmembrane helices in protein structures

Investigating the Product Profiles and Structural Relationships of New Levansucrases with Conventional and Non-Conventional Substrates

Investigation of the impact of PTMs on the protein backbone conformation

Knowledge-based prediction of protein backbone conformation using a structural alphabet

Local dynamics of proteins and DNA evaluated from crystallographic B factors

Local structural differences in homologous proteins: specificities in different SCOP classes

Modeling and molecular dynamics of HPA-1a and -1b polymorphisms: effects on the structure of the β3 subunit of the αIIbβ3 integrin

Modeling and molecular dynamics simulations of the V33 variant of the integrin subunit β3: Structural comparison with the L33 (HPA-1a) and P33 (HPA-1b) variants

Molecular characterization of 13 new RHD alleles.

Multiple interests in structural models of DARC transmembrane protein.

New opportunities to fight against infectious diseases and to identify pertinent drug targets with novel methodologies

ORION: a web server for protein fold recognition and structure prediction using evolutionary hybrid profiles

PRR repeats in the intracellular domain of KISS1R are important for its export to cell membrane.

PTM-SD: a database of structurally resolved and annotated posttranslational modifications in proteins.

PolyprOnline: polyproline helix II and secondary structure assignment database

Predicting protein flexibility through the prediction of local structures

Prediction of the intestinal resistome by a three-dimensional structure-based method

PredyFlexy: flexibility and local structure prediction from sequence.

Progressive structure-based alignment of homologous proteins: Adopting sequence comparison strategies.

Protein Peeling 3D: new tools for analyzing protein structures.

Protein beta-turn assignments

Protein contacts, inter-residue interactions and side-chain modelling.

Protein flexibility in the light of structural alphabets

Protein secondary structure assignment revisited: a detailed analysis of different assignment methods.

Protein short loop prediction in terms of a structural alphabet

Recent advances on polyproline II.

Same but not alike: Structure, flexibility and energetics of domains in multi-domain proteins are influenced by the presence of other domains.

Sequence-structure relationship study in all-α transmembrane proteins using an unsupervised learning approach.