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1

DoSA: Database of Structural Alignments

Mahajan, S., Agarwal, G., Iftekhar, M., Offmann, B., de Brevern, A. G., Srinivasan, N.

Journal:

Year:

2013

Language:

english

File:

PDF, 403 KB

english, 2013

2

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

Craveur, P., Rebehmed, J., de Brevern, A. G.

Journal:

Year:

2014

Language:

english

File:

PDF, 799 KB

english, 2014

3

PolyprOnline: polyproline helix II and secondary structure assignment database

Chebrek, R., Leonard, S., de Brevern, A. G., Gelly, J.-C.

Journal:

Year:

2014

Language:

english

File:

PDF, 1.16 MB

english, 2014

4

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

5

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

6

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

7

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

8

Bayesian probabilistic approach for predicting backbone structures in terms of protein blocks

A.G. de Brevern, C. Etchebest, S. Hazout

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2000

Language:

english

File:

PDF, 414 KB

english, 2000

9

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

10

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

11

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

12

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

13

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

14

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

15

A computational protocol to fragment-based drug design at PDB scale

F Moriaud, T Henry, SA Adcock, AM Vorotynsev, L Martin, O Doppelt, AG De Brevern, F Delfaud

Journal:

Chemistry Central Journal

Year:

2008

Language:

english

File:

PDF, 78 KB

english, 2008

16

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

17

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

18

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

19

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

20

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

21

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

22

Protein structure mining using a structural alphabet

M. Tyagi, A. G. de Brevern, N. Srinivasan, B. Offmann

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2008

Language:

english

File:

PDF, 730 KB

english, 2008

23

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

24

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

25

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

26

Compacting local protein folds with a “hybrid protein model”

A. G. de Brevern, S. Hazout

Journal:

Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta)

Year:

2001

Language:

english

File:

PDF, 491 KB

english, 2001

27

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

C. Etchebest, C. Benros, A. Bornot, A.-C. Camproux, A. G. de Brevern

Journal:

European Biophysics Journal

Year:

2007

Language:

english

File:

PDF, 295 KB

english, 2007

28

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

29

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

30

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

A G de Brevern, C Etchebest, C Benros, S Hazout

Journal:

Journal of Biosciences

Year:

2007

Language:

english

File:

PDF, 1.09 MB

english, 2007

31

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

32

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

33

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

34

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

35

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

36

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

A.G. de Brevern, H. Wong, C. Tournamille, Y. Colin, C. Le Van Kim, C. Etchebest

Journal:

Biochimica et Biophysica Acta (BBA) - General Subjects

Year:

2005

Language:

english

File:

PDF, 992 KB

english, 2005

37

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

38

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

39

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

40

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

41

Multiple interests in structural models of DARC transmembrane protein

D. Smolarek, O. Bertrand, M. Czerwinski, Y. Colin, C. Etchebest, A.G. de Brevern

Journal:

Transfusion Clinique et Biologique

Year:

2010

File:

PDF, 1.08 MB

2010

42

VHHs or nanobodies directed against proteins of the human red cell membrane

D. Smolarek, I. Habib, C. Hattab, S. Cochet, G. Hassanzadeh-Ghassabeh, C. Gutierrez, J. Picot, M. Grodecka, K. Wasniowska, R. Udomsangpetch, A.G. de Brevern, S. Muyldermans, Y. Colin, C. Le Van Kim, M

Journal:

Transfusion Clinique et Biologique

Year:

2010

Language:

english

File:

PDF, 57 KB

english, 2010

43

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

44

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

45

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

46

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

47

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

48

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

49

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

50

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