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1

Optimization of the standard genetic code according to three codon positions using an evolutionary algorithm

Błażej, Paweł, Wnętrzak, Małgorzata, Mackiewicz, Dorota, Mackiewicz, Paweł, de Brevern, Alexandre G.

Journal:

Year:

2018

Language:

english

File:

PDF, 11.01 MB

english, 2018

2

GPU-FS-kNN: A Software Tool for Fast and Scalable kNN Computation Using GPUs

Arefin, Ahmed Shamsul, Riveros, Carlos, Berretta, Regina, Moscato, Pablo, de Brevern, Alexandre G.

Journal:

Year:

2012

Language:

english

File:

PDF, 1.12 MB

english, 2012

3

Effective Automated Feature Construction and Selection for Classification of Biological Sequences

Kamath, Uday, De Jong, Kenneth, Shehu, Amarda, de Brevern, Alexandre G.

Journal:

Year:

2014

Language:

english

File:

PDF, 1.01 MB

english, 2014

4

Waggawagga-CLI: A command-line tool for predicting stable single α-helices (SAH-domains), and the SAH-domain distribution across eukaryotes

Simm, Dominic, Kollmar, Martin, de Brevern, Alexandre G.

Journal:

Year:

2018

Language:

english

File:

PDF, 1.37 MB

english, 2018

5

αIIbβ3 integrin: new allelic variants in Glanzmann thrombasthenia, effects on ITGA2B and ITGB3 mRNA splicing, expression, and structure–function

Vincent Jallu, Mathilde Dusseaux, Simon Panzer, Marie-Françoise Torchet, Nathalie Hezard, Jenny Goudemand, Alexandre G. de Brevern, Cécile Kaplan

Journal:

Year:

2010

Language:

english

File:

PDF, 399 KB

english, 2010

6

Protein short loop prediction in terms of a structural alphabet

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

Journal:

Computational Biology and Chemistry

Year:

2009

Language:

english

File:

PDF, 288 KB

english, 2009

7

Analyzing the sequence–structure relationship of a library of local structural prototypes

Cristina Benros, Alexandre G. de Brevern, Serge Hazout

Journal:

Journal of Theoretical Biology

Year:

2009

Language:

english

File:

PDF, 1.39 MB

english, 2009

8

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

Alexandre G. de Brevern, Agnel Praveen Joseph

Journal:

Journal of Theoretical Biology

Year:

2011

Language:

english

File:

PDF, 1003 KB

english, 2011

9

Genome compartimentation by a Hybrid Chromosome Model (HχM). Application to Saccharomyces cerevisae subtelomeres

Alexandre G. de Brevern, France Loirat, Anne Badel-Chagnon, Cécile André, Pierre Vincens, Serge Hazout

Journal:

Computers & Chemistry

Year:

2002

Language:

english

File:

PDF, 447 KB

english, 2002

10

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

Juliette Martin, Guillaume Letellier, Antoine Marin, Jean-François Taly, Alexandre G de Brevern, Jean-François Gibrat

Journal:

BMC Structural Biology

Year:

2005

Language:

english

File:

PDF, 881 KB

english, 2005

11

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

Ksenia Oguievetskaia, Laetitia Martin-Chanas, Artem Vorotyntsev, Olivia Doppelt-Azeroual, Xavier Brotel, Stewart A Adcock, Alexandre G de Brevern, Francois Delfaud, Fabrice Moriaud

Journal:

Journal of Cheminformatics

Year:

2010

Language:

english

File:

PDF, 145 KB

english, 2010

12

Analysis of loop boundaries using different local structure assignment methods

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

Journal:

Protein Science

Year:

2009

Language:

english

File:

PDF, 459 KB

english, 2009

13

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

Olivia Doppelt-Azeroual, François Delfaud, Fabrice Moriaud, Alexandre G. de Brevern

Journal:

Protein Science

Year:

2010

Language:

english

File:

PDF, 1.57 MB

english, 2010

14

A structural alphabet for local protein structures: Improved prediction methods

Catherine Etchebest, Cristina Benros, Serge Hazout, Alexandre G. de Brevern

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 843 KB

english, 2005

15

Assessing a novel approach for predicting local 3D protein structures from sequence

Cristina Benros, Alexandre G. de Brevern, Catherine Etchebest, Serge Hazout

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 1.22 MB

english, 2006

16

In silico local structure approach: A case study on Outer Membrane Proteins

Juliette Martin, Alexandre G. de Brevern, Anne-Claude Camproux

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.19 MB

english, 2008

17

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

Aurélie Bornot, Catherine Etchebest, Alexandre G. de Brevern

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2009

Language:

english

File:

PDF, 466 KB

english, 2009

18

Predicting protein flexibility through the prediction of local structures

Aurélie Bornot, Catherine Etchebest, Alexandre G. de Brevern

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2011

Language:

english

File:

PDF, 803 KB

english, 2011

19

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

Dorota Smolarek, Claude Hattab, Gholamreza Hassanzadeh-Ghassabeh, Sylvie Cochet, Carlos Gutiérrez, Alexandre G. de Brevern, Rachanee Udomsangpetch, Julien Picot, Magdalena Grodecka, Kazimiera Wasniows

Journal:

Cellular and Molecular Life Sciences

Year:

2010

Language:

english

File:

PDF, 837 KB

english, 2010

20

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

Jean Pylouster, Aurélie Bornot, Catherine Etchebest, Alexandre G. de Brevern

Journal:

Year:

2010

Language:

english

File:

PDF, 971 KB

english, 2010

21

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

Ksenia Oguievetskaia, Laetitia Martin-Chanas, Artem Vorotyntsev, Olivia Doppelt-Azeroual, Xavier Brotel, Stewart A. Adcock, Alexandre G. de Brevern, Francois Delfaud, Fabrice Moriaud

Journal:

Journal of Computer-Aided Molecular Design

Year:

2009

Language:

english

File:

PDF, 364 KB

english, 2009

22

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

Alexandre G. de Brevern, Hélène Valadié, Serge Hazout, Catherine Etchebest

Journal:

Protein Science

Year:

2002

Language:

english

File:

PDF, 550 KB

english, 2002

23

A Dominant Mutation in the Gene Encoding the Erythroid Transcription Factor KLF1 Causes a Congenital Dyserythropoietic Anemia

Lionel Arnaud, Carole Saison, Virginie Helias, Nicole Lucien, Dominique Steschenko, Marie-Catherine Giarratana, Claude Prehu, Bernard Foliguet, Lory Montout, Alexandre G. de Brevern, Alain Francina, P

Journal:

The American Journal of Human Genetics

Year:

2010

Language:

english

File:

PDF, 752 KB

english, 2010

24

Influence of microarrays experiments missing values on the stability of gene groups by hierarchical clustering

Alexandre G de Brevern, Serge Hazout, Alain Malpertuy

Journal:

BMC Bioinformatics

Year:

2004

Language:

english

File:

PDF, 888 KB

english, 2004

25

Use of a structural alphabet for analysis of short loops connecting repetitive structures

Laurent Fourrier, Cristina Benros, Alexandre G de Brevern

Journal:

BMC Bioinformatics

Year:

2004

Language:

english

File:

PDF, 1.60 MB

english, 2004

26

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

Magalie Celton, Alain Malpertuy, Gaëlle Lelandais, Alexandre G de Brevern

Journal:

Year:

2010

Language:

english

File:

PDF, 1.54 MB

english, 2010

27

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

Guilhem Faure, Aurélie Bornot, Alexandre G. de Brevern

Journal:

Year:

2008

Language:

english

File:

PDF, 841 KB

english, 2008

28

Corrigendum to “Protein contacts, inter-residue interactions and side-chain modelling” [Biochimie 90 (4) (2008) 626–639]

Guilhem Faure, Aurélie Bornot, Alexandre G. de Brevern

Journal:

Year:

2008

Language:

english

File:

PDF, 63 KB

english, 2008

29

Analysis of protein contacts into Protein Units

Guilhem Faure, Aurélie Bornot, Alexandre G. de Brevern

Journal:

Year:

2009

Language:

english

File:

PDF, 867 KB

english, 2009

30

Improvement of protein structure comparison using a structural alphabet

Agnel Praveen Joseph, N. Srinivasan, Alexandre G. de Brevern

Journal:

Year:

2011

Language:

english

File:

PDF, 1.23 MB

english, 2011

31

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

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

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 232 KB

english, 2006

32

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

Joseph, Agnel Praveen, Srinivasan, Narayanaswamy, de Brevern, Alexandre G.

Journal:

Year:

2012

Language:

english

File:

PDF, 1.80 MB

english, 2012

33

Bioinformatic Analysis of the Protein/DNA Interface

Schneider, Bohdan, Černý, Jiří, Svozil, Daniel, Joseph, Agnel Praveen, Gelly, Jean-Christophe, de Brevern, Alexandre G.

Journal:

Biophysical Journal

Year:

2011

Language:

english

File:

PDF, 37 KB

english, 2011

34

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

Swapna, Lakshmipuram S, Mahajan, Swapnil, de Brevern, Alexandre G, Srinivasan, Narayanaswamy

Journal:

BMC Structural Biology

Year:

2012

Language:

english

File:

PDF, 1.21 MB

english, 2012

35

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

Bhaskara, Ramachandra M., de Brevern, Alexandre G., Srinivasan, Narayanaswamy

Journal:

Journal of Biomolecular Structure and Dynamics

Year:

2013

Language:

english

File:

PDF, 574 KB

english, 2013

36

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

Léonard, Sylvain, Joseph, Agnel Praveen, Srinivasan, Narayanaswamy, Gelly, Jean-Christophe, de Brevern, Alexandre G.

Journal:

Journal of Biomolecular Structure and Dynamics

Year:

2014

Language:

english

File:

PDF, 420 KB

english, 2014

37

Cis–transpeptide variations in structurally similar proteins

Agnel Praveen Joseph, Narayanaswamy Srinivasan, Alexandre G. de Brevern

Journal:

Year:

2012

Language:

english

File:

PDF, 1.19 MB

english, 2012

38

β-bulges: Extensive structural analyses of β-sheets irregularities

Craveur, Pierrick, Joseph, Agnel Praveen, Rebehmed, Joseph, de Brevern, Alexandre G.

Journal:

Protein Science

Year:

2013

Language:

english

File:

PDF, 799 KB

english, 2013

39

Evolution study of the Baeyer–Villiger monooxygenases enzyme family: Functional importance of the highly conserved residues

Rebehmed, Joseph, Alphand, Véronique, de Berardinis, Véronique, de Brevern, Alexandre G.

Journal:

Year:

2013

Language:

english

File:

PDF, 1.95 MB

english, 2013

40

A Novel Evaluation of Residue and Protein Volumes by Means of Laguerre Tessellation

Esque, Jeremy, Oguey, Christophe, de Brevern, Alexandre G.

Journal:

Journal of Chemical Information and Modeling

Year:

2010

Language:

english

File:

PDF, 3.52 MB

english, 2010

41

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

Jallu, Vincent, Poulain, Pierre, Fuchs, Patrick F.J., Kaplan, Cecile, de Brevern, Alexandre G.

Journal:

Year:

2014

Language:

english

File:

PDF, 1.82 MB

english, 2014

42

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

Mahajan, Swapnil, de Brevern, Alexandre G., Sanejouand, Yves-Henri, Srinivasan, Narayanaswamy, Offmann, Bernard

Journal:

Protein Science

Year:

2015

Language:

english

File:

PDF, 9.16 MB

english, 2015

43

Comparative Analysis of Threshold and Tessellation Methods for Determining Protein Contacts

Esque, Jeremy, Oguey, Christophe, de Brevern, Alexandre G.

Journal:

Journal of Chemical Information and Modeling

Year:

2011

Language:

english

File:

PDF, 3.79 MB

english, 2011

44

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

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

Journal:

Journal of Biomolecular Structure and Dynamics

Year:

2014

Language:

english

File:

PDF, 521 KB

english, 2014

45

Local dynamics of proteins and DNA evaluated from crystallographic B factors

Schneider, Bohdan, Gelly, Jean-Christophe, de Brevern, Alexandre G., Černý, Jiří

Journal:

Acta Crystallographica Section D Biological Crystallography

Year:

2014

Language:

english

File:

PDF, 195 KB

english, 2014

46

PRR Repeats in the Intracellular Domain of KISS1R Are Important for Its Export to Cell Membrane

Chevrier, Lucie, de Brevern, Alexandre, Hernandez, Eva, Leprince, Jérome, Vaudry, Hubert, Guedj, Anne Marie, de Roux, Nicolas

Journal:

Molecular Endocrinology

Year:

2013

Language:

english

File:

PDF, 1.89 MB

english, 2013

47

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

Esque, Jérémy, Urbain, Aurélie, Etchebest, Catherine, de Brevern, Alexandre G.

Journal:

Year:

2015

Language:

english

File:

PDF, 3.56 MB

english, 2015

48

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

Kalaivani, Raju, de Brevern, Alexandre G., Srinivasan, Narayanaswamy

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2016

Language:

english

File:

PDF, 1.40 MB

english, 2016

49

Cover Image, Volume 84, Issue 7

Kalaivani, Raju, de Brevern, Alexandre G., Srinivasan, Narayanaswamy

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2016

File:

PDF, 2.49 MB

2016

50

Global analysis of VHHs framework regions with a structural alphabet

Noel, Floriane, Malpertuy, Alain, de Brevern, Alexandre G.

Journal:

Year:

2016

Language:

english

File:

PDF, 1.86 MB

english, 2016

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