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Alexandre G. de Brevern

154
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Molecular dynamics of the human RhD and RhAG blood group proteins

Aline Floch , Tatiana Galochkina , France Pirenne , Christophe Tournamille , Alexandre G de Brevern
Frontiers in Chemistry, 2024, 12, pp.1360392. ⟨10.3389/fchem.2024.1360392⟩
Article dans une revue inserm-04510947v1
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HumanLectome, an update of UniLectin for the annotation and prediction of human lectins

Boris Schnider , Yacine M’rad , Jalaa El Ahmadie , Alexandre G de Brevern , Anne Imberty
Nucleic Acids Research, 2024, 52 (D1), pp.D1683 - D1693. ⟨10.1093/nar/gkad905⟩
Article dans une revue hal-04376368v1
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A perspective on the sharing of docking data

Samia Aci-Sèche , Stéphane Bourg , Pascal Bonnet , Joseph Rebehmed , Alexandre de Brevern
Data in Brief, 2023, 49 (22), pp.109386. ⟨10.1016/j.dib.2023.109386⟩
Article dans une revue hal-04251910v1

Structural Space of the Duffy Antigen/Receptor for Chemokines’ Intrinsically Disordered Ectodomain 1 Explored by Temperature Replica-Exchange Molecular Dynamics Simulations

Agata Kranjc , Tarun Jairaj Narwani , Sophie Abby , Alexandre de Brevern
International Journal of Molecular Sciences, 2023, 24 (17), pp.13280. ⟨10.3390/ijms241713280⟩
Article dans une revue hal-04256911v1
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General Trends of the Camelidae Antibody VHHs Domain Dynamics

Akhila Melarkode Vattekatte , Julien Diharce , Joseph Rebehmed , Frédéric Cadet , Fabrice Gardebien
International Journal of Molecular Sciences, 2023, 24, pp.4511. ⟨10.3390/ijms24054511⟩
Article dans une revue inserm-04258550v1
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AlphaFold2 Update and Perspectives

Sébastien Tourlet , Ragousandirane Radjasandirane , Julien Diharce , Alexandre G de Brevern
BioMedInformatics, 2023, 3, pp.378 - 390. ⟨10.3390/biomedinformatics3020025⟩
Article dans une revue inserm-04258522v1
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BioMedInformatics, the Link between Biomedical Informatics, Biology and Computational Medicine

Alexandre G de Brevern
BioMedInformatics, 2023, 4, pp.1 - 7. ⟨10.3390/biomedinformatics4010001⟩
Article dans une revue inserm-04510907v1
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VHH Structural Modelling Approaches: A Critical Review

Poonam Vishwakarma , Akhila Melarkode Vattekatte , Nicolas Shinada , Julien Diharce , Carla Martins
International Journal of Molecular Sciences, 2022, 23 (7), pp.3721. ⟨10.3390/ijms23073721⟩
Article dans une revue hal-03665842v1
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Analysis of Integrin αIIb Subunit Dynamics Reveals Long-Range Effects of Missense Mutations on Calf Domains

Sali Anies , Vincent Jallu , Julien Diharce , Tarun J Narwani , Alexandre G de Brevern
International Journal of Molecular Sciences, 2022, 23 (2), pp.858. ⟨10.3390/ijms23020858⟩
Article dans une revue hal-03542900v1

SWORD2: hierarchical analysis of protein 3D structures

Gabriel Cretin , Tatiana Galochkina , Yann Vander Meersche , Alexandre G de Brevern , Guillaume Postic
Nucleic Acids Research, 2022, 50 (W1), pp.W732--W738. ⟨10.1093/nar/gkac370⟩
Article dans une revue hal-03738483v1

New αIIbβ3 variants in 28 Turkish Glanzmann patients; structural hypothesis for complex activation by residues variations in I-EGF domains

M Koker , N Sarper , C Albayrak , B Zulfikar , E Zengin
Platelets, 2022, 33 (4), pp.551-561. ⟨10.1080/09537104.2021.1947481⟩
Article dans une revue hal-03684658v1

CALR-ETdb, the database of calreticulin variants diversity in essential thrombocythemia

Nora El Jahrani , Gabriel Cretin , Alexandre de Brevern
Platelets, 2022, 33 (1), pp.157-167. ⟨10.1080/09537104.2020.1869712⟩
Article dans une revue hal-03695851v1

Prediction of structural alphabet protein blocks using data mining

Mirjana Maljković , Nenad Mitić , Alexandre de Brevern
Biochimie, 2022, 197, pp.74-85. ⟨10.1016/j.biochi.2022.01.019⟩
Article dans une revue hal-03652564v1

Current status of PTMs structural databases: applications, limitations and prospects

Alexandre de Brevern , Joseph Rebehmed
Amino Acids, 2022, 54 (4), pp.575-590. ⟨10.1007/s00726-021-03119-z⟩
Article dans une revue hal-03690712v1

PYTHIA: Deep Learning Approach for Local Protein Conformation Prediction

Gabriel Cretin , Tatiana Galochkina , Alexandre de Brevern , Jean-Christophe Gelly
International Journal of Molecular Sciences, 2021, 22 (16), pp.8831. ⟨10.3390/ijms22168831⟩
Article dans une revue hal-03822577v1
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A Review of the Literature Organized Into a New Database: RHeference

Aline Floch , Stéphane Téletchéa , Christophe Tournamille , Alexandre de Brevern , France Pirenne
Transfusion Medicine Reviews, 2021, 35 (2), pp.70-77. ⟨10.1016/j.tmrv.2021.04.002⟩
Article dans une revue inserm-03253477v1

Insights into Comparative Modeling of VHH Domains

Akhila Melarkode Vattekatte , Frédéric Cadet , Jean-Christophe Gelly , Alexandre de Brevern
International Journal of Molecular Sciences, 2021, 22 (18), pp.9771. ⟨10.3390/ijms22189771⟩
Article dans une revue hal-03537422v1
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Insights into anti‐D formation in carriers of RhD variants through studies of 3D intraprotein interactions

Aline Floch , France Pirenne , Aurélie Barrault , Btissam Chami , Cécile Toly‐ndour
Transfusion, 2021, 61 (4), pp.1286-1301. ⟨10.1111/trf.16301⟩
Article dans une revue inserm-03253510v1
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ABCG2 Is Overexpressed on Red Blood Cells in Ph-Negative Myeloproliferative Neoplasms and Potentiates Ruxolitinib-Induced Apoptosis

Ralfs Buks , Mégane Brusson , Sylvie Cochet , Tatiana Galochkina , Bruno Cassinat
International Journal of Molecular Sciences, 2021, 22 (7), pp.3530. ⟨10.3390/ijms22073530⟩
Article dans une revue hal-03531056v1

Structural and evolutionary exploration of the IL-3 family and its alpha subunit receptors

Jade Fogha , Jagadeesh Bayry , Julien Diharce , Alexandre de Brevern
Amino Acids, 2021, 53 (8), pp.1211-1227. ⟨10.1007/s00726-021-03026-3⟩
Article dans une revue hal-03538521v1
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Transient association between proteins elicits alteration of dynamics at sites far away from interfaces

Himani Tandon , Alexandre de Brevern , Narayanaswamy Srinivasan
Structure, 2021, 29 (4), pp.371-384.e3. ⟨10.1016/j.str.2020.11.015⟩
Article dans une revue inserm-03543689v1

Hierarchical Structure of Protein Sequence

Alexei Nekrasov , Yuri Kozmin , Sergey Kozyrev , Rustam Ziganshin , Alexandre de Brevern
International Journal of Molecular Sciences, 2021, 22 (15), pp.8339. ⟨10.3390/ijms22158339⟩
Article dans une revue hal-03538152v1

Conformational Strain Indicated by Ramachandran Angles for the Protein Backbone Is Only Weakly Related to the Flexibility

Ashraya Ravikumar , Alexandre de Brevern , Narayanaswamy Srinivasan
Journal of Physical Chemistry B, 2021, 125 (10), pp.2597-2606. ⟨10.1021/acs.jpcb.1c00168⟩
Article dans une revue hal-03549944v1
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Discrete analysis of camelid variable domains: sequences, structures, and in-silico structure prediction

Akhila Melarkode Vattekatte , Nicolas Ken Shinada , Tarun J Narwani , Floriane Noël , Olivier Bertrand
PeerJ, 2020, 8, pp.e8408. ⟨10.7717/peerj.8408⟩
Article dans une revue inserm-02907323v1
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Accurate Representation of Protein-Ligand Structural Diversity in the Protein Data Bank (PDB)

Nicolas K Shinada , Peter Schmidtke , Alexandre de Brevern
International Journal of Molecular Sciences, 2020, 21 (6), pp.2243. ⟨10.3390/ijms21062243⟩
Article dans une revue inserm-02907370v1
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Analysis of Protein Disorder Predictions in the Light of a Protein Structural Alphabet

Alexandre de Brevern
Biomolecules, 2020, 10 (7), pp.1080. ⟨10.3390/biom10071080⟩
Article dans une revue inserm-02907391v1
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Data set of intrinsically disordered proteins analysed at a local protein conformation level

Akhila Melarkode Vattekatte , Tarun Jairaj Narwani , Aline Floch , Mirjana Maljković , Soubika Bisoo
Data in Brief, 2020, 29, pp.105383. ⟨10.1016/j.dib.2020.105383⟩
Article dans une revue inserm-02907359v1
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A structural entropy index to analyse local conformations in intrinsically disordered proteins

Akhila Melarkode Vattekatte , Tarun Jairaj Narwani , Aline Floch , Mirjana Maljković , Soubika Bisoo
Journal of Structural Biology, 2020, 210 (1), pp.107464. ⟨10.1016/j.jsb.2020.107464⟩
Article dans une revue inserm-02907335v1
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Investigating the Product Profiles and Structural Relationships of New Levansucrases with Conventional and Non-Conventional Substrates

Andrea Hill , Salwa Karboune , Tarun Narwani , Alexandre de Brevern
International Journal of Molecular Sciences, 2020, 21 (15), pp.5402. ⟨10.3390/ijms21155402⟩
Article dans une revue inserm-02913693v1
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Investigation of the impact of PTMs on the protein backbone conformation

Pierrick Craveur , Tarun Narwani , Joseph Rebehmed , Alexandre de Brevern
Amino Acids, 2019, 51 (7), pp.1065-1079. ⟨10.1007/s00726-019-02747-w⟩
Article dans une revue inserm-02266176v1

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

Anna Guadall , Sylvie Cochet , Olivier Renaud , Yves Colin , Caroline Le van Kim
Journal of Biological Chemistry, 2019, 294 (41), pp.14911-14921. ⟨10.1074/jbc.RA119.007521⟩
Article dans une revue hal-02416861v1
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Long-range molecular dynamics show that inactive forms of Protein Kinase A are more dynamic than active forms

R. Kalaivani , T. J Narwani , Alexandre de Brevern , N. Srinivasan
Protein Science, 2019, 28 (3), pp.543-560. ⟨10.1002/pro.3556⟩
Article dans une revue inserm-02913871v1
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Discrete analyses of protein dynamics

Akhila Melarkode Vattekatte , Tarun Jairaj Narwani , Pierrick Craveur , Nicolas K Shinada , Aline Floch
Journal of Biomolecular Structure and Dynamics, 2019, pp.1-15. ⟨10.1080/07391102.2019.1650112⟩
Article dans une revue inserm-02266159v1

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

Etienne Ruppé , Amine Ghozlane , Julien Tap , Nicolas Pons , Anne-Sophie Alvarez
Nature Microbiology, 2019, 4 (1), pp.112-123. ⟨10.1038/s41564-018-0292-6⟩
Article dans une revue pasteur-02552015v1
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Short in-Frame Insertions/Deletions in the Coding Sequence of the α-Globin Gene. Consequences of the 3D Structure and Resulting Phenotypes: Hb Choisy as an Example

Henri Wajcman , Alexandre de Brevern , Jean Riou , Céline Latouche , Michael C. Marden
Hemoglobin, 2019, 42 (5-6), pp.287-293. ⟨10.1080/03630269.2018.1556683⟩
Article dans une revue inserm-02913864v1
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A minimum set of stable blocks for rational design of polypeptide chains Running head: A set of stable blocks for protein rational design

Alexei N Nekrasov , Ludmila G Alekseeva , Rudolf А. Pogosyan , Dmitry A Dolgikh , M.P. P Kirpichnikov
Biochimie, 2019, 160, pp.88-92. ⟨10.1016/j.biochi.2019.02.006⟩
Article dans une revue inserm-02266188v1
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iPBAvizu: a PyMOL plugin for an efficient 3D protein structure superimposition approach

Guilhem Faure , Agnel Praveen Joseph , Pierrick Craveur , Tarun Narwani , Narayanaswamy Srinivasan
Source Code for Biology and Medicine, 2019, 14 (1), ⟨10.1186/s13029-019-0075-3⟩
Article dans une revue inserm-02913723v1
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Benchmarking the PEPOP methods for mimicking discontinuous epitopes

Vincent Demolombe , Alexandre de Brevern , Franck Molina , Géraldine Lavigne , Claude Granier
BMC Bioinformatics, 2019, 20 (1), pp.738. ⟨10.1186/s12859-019-3189-3⟩
Article dans une revue hal-02787607v2
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Halogens in Protein−Ligand Binding Mechanism: A Structural Perspective

Nicolas Shinada , Alexandre de Brevern , Peter Schmidtke
Journal of Medicinal Chemistry, 2019, 62 (21), pp.9341-9356. ⟨10.1021/acs.jmedchem.8b01453⟩
Article dans une revue inserm-02913756v1
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PEPOP 2.0: new approaches to mimic non-continuous epitopes

Vincent Demolombe , Alexandre de Brevern , Liza L. Felicori , Christophe Nguyen , Ricardo Andrez Machado de Avila
BMC Bioinformatics, 2019, 20 (1), ⟨10.1186/s12859-019-2867-5⟩
Article dans une revue hal-02277257v1
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Structural variations within proteins can be as large as variations observed across their homologues

Iyanar Vetrivel , Alexandre de Brevern , Frédéric Cadet , Narayanaswamy Srinivasan , Bernard Offmann
Biochimie, 2019, 167, pp.162-170. ⟨10.1016/j.biochi.2019.09.013⟩
Article dans une revue inserm-02913845v1
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In silico prediction of protein flexibility with local structure approach

Tarun J. Narwani , Catherine Etchebest , Pierrick Craveur , Sylvain Léonard , Joseph Rebehmed
Biochimie, 2019, 165, pp.150-155. ⟨10.1016/j.biochi.2019.07.025⟩
Article dans une revue inserm-02266143v1
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Dynamics and deformability of α-, 310- and π-helices

Tarun Narwani , Pierrick Craveur , Nicolas Shinada , Hubert Santuz , Joseph Rebehmed
Archives of Biological Science, 2018, 70 (1), pp.21-31. ⟨10.2298/ABS170215022N⟩
Article dans une revue inserm-01585114v1
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Same but not alike: Structure, flexibility and energetics of domains in multi-domain proteins are influenced by the presence of other domains

Sneha Vishwanath , Alexandre de Brevern , Narayanaswamy Srinivasan
PLoS Computational Biology, 2018, 14 (2), pp.e1006008. ⟨10.1371/journal.pcbi.1006008⟩
Article dans une revue inserm-02147944v1
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Analysing the Structural Effect of Point Mutations of Cytotoxic Necrotizing Factor 1 (CNF1) on Lu/BCAM Adhesion Glycoprotein Association

Alexandre de Brevern
Toxins, 2018, 10 (3), pp.E122. ⟨10.3390/toxins10030122⟩
Article dans une revue inserm-01852766v1

Protein local conformations at the light of a structural alphabet

Alexandre de Brevern
Biophysical Journal, 2018, 114 (3), pp.231A. ⟨10.1016/j.bpj.2017.11.1286⟩
Article dans une revue inserm-01852960v1
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Knowledge-based prediction of protein backbone conformation using a structural alphabet

Iyanar Vetrivel , Swapnil Mahajan , Manoj Tyagi , Lionel Hoffmann , Yves-Henri Sanejouand
PLoS ONE, 2017, 12 (11), pp.e0186215. ⟨10.1371/journal.pone.0186215⟩
Article dans une revue hal-01677391v1
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Recent advances on polyproline II.

Tarun Jairaj Narwani , Hubert Santuz , Nicolas Shinada , Akhila Melarkode Vattekatte , Yassine Ghouzam
Amino Acids, 2017, 49 (4), pp.705-713. ⟨10.1007/s00726-017-2385-6⟩
Article dans une revue inserm-01573940v1
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Molecular characterization of 13 new RHD alleles

Aline Floch , Aurelie Barrault , Alexandre de Brevern , Jennifer Martret , Kevin Gaillard
Transfusion, 2017, 57 (4), pp. 1089-1091. ⟨10.1111/trf.14004⟩
Article dans une revue hal-01627823v1
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Global analysis of VHHs framework regions with a structural alphabet

Floriane Noël , Alain Malpertuy , Alexandre de Brevern
Biochimie, 2016, 131, pp.11 - 19. ⟨10.1016/j.biochi.2016.09.005⟩
Article dans une revue inserm-01374633v1
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Extension of the classical classification of β-turns

Alexandre de Brevern
Scientific Reports, 2016, pp.33191 ⟨10.1038/srep33191⟩
Article dans une revue inserm-01374651v1

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

Swapnil Mahajan , Alexandre de Brevern , Yves-Henri Sanejouand , Narayanaswamy Srinivasan , Bernard Offmann
Protein Science, 2015, 24 (1), pp.145 - 153. ⟨10.1002/pro.2581⟩
Article dans une revue hal-01677393v1
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Correlation between local structural dynamics of proteins inferred from NMR ensembles and evolutionary dynamics of homologues of known structure.

Swapnil Mahajan , Alexandre de Brevern , Bernard Offmann , Narayanaswamy Srinivasan
Journal of Biomolecular Structure and Dynamics, 2014, 32 (5), pp.751-8. ⟨10.1080/07391102.2013.789989⟩
Article dans une revue inserm-00926204v1
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mulPBA: an efficient multiple protein structure alignment method based on a structural alphabet.

Sylvain Léonard , Agnel Praveen Joseph , Narayanaswamy Srinivasan , Jean-Christophe Gelly , Alexandre de Brevern
Journal of Biomolecular Structure and Dynamics, 2014, 32 (4), pp.661-8. ⟨10.1080/07391102.2013.787026⟩
Article dans une revue inserm-00926338v1
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Bioinformatic analysis of the protein/DNA interface.

Bohdan Schneider , Jirí Cerny , Daniel Svozil , Petr Cech , Jean-Christophe Gelly
Nucleic Acids Research, 2014, 42 (5), pp.3381-94. ⟨10.1093/nar/gkt1273⟩
Article dans une revue inserm-00926088v1
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PRR repeats in the intracellular domain of KISS1R are important for its export to cell membrane.

Lucie Chevrier , Alexandre de Brevern , Eva Hernandez , Jérome Leprince , Hubert Vaudry
Mol Endocrinol, 2013, 27 (6), pp.1004-14. ⟨10.1210/me.2012-1386⟩
Article dans une revue inserm-00926577v1
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Evolution study of the Baeyer-Villiger monooxygenases enzyme family: functional importance of the highly conserved residues.

Joseph Rebehmed , Véronique Alphand , Véronique de Berardinis , Alexandre de Brevern
Biochimie, 2013, 95 (7), pp.1394-402. ⟨10.1016/j.biochi.2013.03.005⟩
Article dans une revue inserm-00926584v1
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DoSA: Database of Structural Alignments.

Swapnil Mahajan , Garima Agarwal , Mohammed Iftekhar , Bernard Offmann , Alexandre de Brevern
Database - The journal of Biological Databases and Curation, 2013, 2013, pp.bat048. ⟨10.1093/database/bat048⟩
Article dans une revue inserm-00926452v1
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Understanding the role of domain-domain linkers in the spatial orientation of domains in multi-domain proteins.

Ramachandra M Bhaskara , Alexandre de Brevern , Narayanaswamy Srinivasan
Journal of Biomolecular Structure and Dynamics, 2013, 31 (12), pp.1467-80. ⟨10.1080/07391102.2012.743438⟩
Article dans une revue inserm-00926595v1
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β-Bulges: extensive structural analyses of β-sheets irregularities.

Pierrick Craveur , Agnel Praveen Joseph , Joseph Rebehmed , Alexandre de Brevern
Protein Science, 2013, 22 (10), pp.1366-78. ⟨10.1002/pro.2324⟩
Article dans une revue inserm-00926388v1
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Cis-trans isomerization of omega dihedrals in proteins.

Pierrick Craveur , Agnel Praveen Joseph , Pierre Poulain , Joseph Rebehmed , Alexandre de Brevern
Amino Acids, 2013, 45 (2), pp.279-89. ⟨10.1007/s00726-013-1511-3⟩
Article dans une revue inserm-00926521v1
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VLDP web server: a powerful geometric tool for analysing protein structures in their environment.

Jérémy Esque , Sylvain Léonard , Alexandre de Brevern , Christophe Oguey
Nucleic Acids Research, 2013, 41 (Web Server issue), pp.W373-8. ⟨10.1093/nar/gkt509⟩
Article dans une revue inserm-00926547v1
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Comparison of tertiary structures of proteins in protein-protein complexes with unbound forms suggests prevalence of allostery in signalling proteins.

Lakshmipuram S. Swapna , Swapnil Mahajan , Alexandre de Brevern , Narayanaswamy Srinivasan
BMC Structural Biology, 2012, 12 (1), pp.6. ⟨10.1186/1472-6807-12-6⟩
Article dans une revue inserm-00725334v1
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Cis-trans peptide variations in structurally similar proteins.

Agnel Praveen Joseph , Narayanaswamy Srinivasan , Alexandre de Brevern
Amino Acids, 2012, 43 (3), pp.1369-81. ⟨10.1007/s00726-011-1211-9⟩
Article dans une revue inserm-00680773v1
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PredyFlexy: flexibility and local structure prediction from sequence.

Alexandre de Brevern , Aurélie Bornot , Pierrick Craveur , Catherine Etchebest , Jean-Christophe Gelly
Nucleic Acids Research, 2012, 40 (Web Server issue), pp.W317-22. ⟨10.1093/nar/gks482⟩
Article dans une revue inserm-00750270v1
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Progressive structure-based alignment of homologous proteins: Adopting sequence comparison strategies.

Agnel Praveen Joseph , Narayanaswamy Srinivasan , Alexandre de Brevern
Biochimie, 2012, 94 (9), pp.2025-34. ⟨10.1016/j.biochi.2012.05.028⟩
Article dans une revue inserm-00750325v1
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Selective constraint on human pre-mRNA splicing by protein structural properties.

Jean-Christophe Gelly , Hsuan-Yu Lin , Alexandre de Brevern , Trees-Juen Chuang , Feng-Chi Chen
Genome Biology and Evolution, 2012, 4 (9), pp.966-75. ⟨10.1093/gbe/evs071⟩
Article dans une revue inserm-00750397v1
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Local structural differences in homologous proteins: specificities in different SCOP classes.

Agnel Praveen Joseph , Hélène Valadié , Narayanaswamy Srinivasan , Alexandre de Brevern
PLoS ONE, 2012, 7 (6), pp.e38805. ⟨10.1371/journal.pone.0038805⟩
Article dans une revue inserm-00750286v1
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Modeling and molecular dynamics of HPA-1a and -1b polymorphisms: effects on the structure of the β3 subunit of the αIIbβ3 integrin.

Vincent Jallu , Pierre Poulain , Patrick F. J. Fuchs , Cécile Kaplan , Alexandre de Brevern
PLoS ONE, 2012, 7 (11), pp.e47304. ⟨10.1371/journal.pone.0047304⟩
Article dans une revue inserm-00926600v1
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Protein Peeling 3D: new tools for analyzing protein structures.

Jean-Christophe Gelly , Alexandre de Brevern
Bioinformatics, 2011, 27 (1), pp.132-3. ⟨10.1093/bioinformatics/btq610⟩
Article dans une revue inserm-00568165v1
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Species specific amino acid sequence - Protein local structure relationships: An analysis in the light of a structural alphabet

Alexandre de Brevern , Agnel Praveen Joseph , Hélène Valadié
Journal of Theoretical Biology, 2011, 276 (1), pp.209. ⟨10.1016/j.jtbi.2011.01.047⟩
Article dans une revue hal-00682413v1
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Assignment of PolyProline II Conformation and Analysis of Sequence - Structure Relationship.

Yohann Mansiaux , Agnel Praveen Joseph , Jean-Christophe Gelly , Alexandre de Brevern
PLoS ONE, 2011, 6 (3), pp.e18401. ⟨10.1371/journal.pone.0018401⟩
Article dans une revue inserm-00586725v1
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Comparative analysis of threshold and tessellation methods for determining protein contacts.

Jeremy Esque , Christophe Oguey , Alexandre de Brevern
Journal of Chemical Information and Modeling, 2011, 51 (2), pp.493-507. ⟨10.1021/ci100195t⟩
Article dans une revue inserm-00568174v1
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Le cahier de laboratoire électronique (CLE)

Anabelle Amiard , Céline Baczynski , Christophe Blanchet , Alexandre de Brevern , Emmanuelle Dorlanne-Messiaen
STP Pharma Pratiques, 2011, 21 (6), pp.475-503
Article dans une revue inserm-00680791v1
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iPBA: a tool for protein structure comparison using sequence alignment strategies.

Jean-Christophe Gelly , Agnel Praveen Joseph , Narayanaswamy Srinivasan , Alexandre de Brevern
Nucleic Acids Research, 2011, 39 (Web Server issue), pp.W18-23. ⟨10.1093/nar/gkr333⟩
Article dans une revue inserm-00646241v1
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Improvement of protein structure comparison using a structural alphabet.

Agnel Praveen Joseph , Narayanaswamy Srinivasan , Alexandre de Brevern
Biochimie, 2011, 93 (9), pp.1434-45. ⟨10.1016/j.biochi.2011.04.010⟩
Article dans une revue inserm-00646245v1
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Identification of local conformational similarity in structurally variable regions of homologous proteins using protein blocks.

Garima Agarwal , Swapnil Mahajan , Narayanaswamy Srinivasan , Alexandre de Brevern
PLoS ONE, 2011, 6 (3), pp.e17826. ⟨10.1371/journal.pone.0017826⟩
Article dans une revue inserm-00586691v1
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Predicting protein flexibility through the prediction of local structures.

Aurélie Bornot , Catherine Etchebest , Alexandre de Brevern
Proteins - Structure, Function and Bioinformatics, 2011, 79 (3), pp.839-52. ⟨10.1002/prot.22922⟩
Article dans une revue inserm-00568171v1
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Species specific amino acid sequence-protein local structure relationships: An analysis in the light of a structural alphabet.

Alexandre de Brevern , Agnel Praveen Joseph
Journal of Theoretical Biology, 2011, 276 (1), pp.209-17. ⟨10.1016/j.jtbi.2011.01.047⟩
Article dans une revue inserm-00646218v1
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Fast and automated functional classification with MED-SuMo: an application on purine-binding proteins.

Olivia Doppelt-Azeroual , François Delfaud , Fabrice Moriaud , Alexandre de Brevern
Protein Science, 2010, 19 (4), pp.847-67. ⟨10.1002/pro.364⟩
Article dans une revue inserm-00458093v1
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Multiple interests in structural models of DARC transmembrane protein.

Dorota Smolarek , Olivier Bertrand , Marcin Czerwinski , Yves Colin , Catherine Etchebest
Transfusion Clinique et Biologique, 2010, 17 (3), pp.184-96. ⟨10.1016/j.tracli.2010.05.003⟩
Article dans une revue inserm-00506537v1
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AlphaIIbbeta3 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
Human Mutation, 2010, 31 (3), pp.237-46. ⟨10.1002/humu.21179⟩
Article dans une revue inserm-00448024v1
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3D Structural Models of Transmembrane Proteins.

Alexandre de Brevern
Methods in Molecular Biology, 2010, 654, pp.387-401. ⟨10.1007/978-1-60761-762-4_20⟩
Article dans une revue inserm-00507094v1
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A novel evaluation of residue and protein volumes by means of Laguerre tessellation.

Jeremy Esque , Christophe Oguey , Alexandre de Brevern
Journal of Chemical Information and Modeling, 2010, 50 (5), pp.947-60. ⟨10.1021/ci9004892⟩
Article dans une revue inserm-00473943v1
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A short survey on protein blocks.

Agnel Joseph , Garima Agarwal , Swapnil Mahajan , Jean-Christophe Gelly , Lakshmipuram S. Swapna
Biophysical Reviews, 2010, 2 (3), pp.137-147. ⟨10.1007/s12551-010-0036-1⟩
Article dans une revue inserm-00512823v1
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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
American Journal of Human Genetics, 2010, 87 (5), pp.721-7. ⟨10.1016/j.ajhg.2010.10.010⟩
Article dans une revue inserm-00550723v1
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Influence of assignment on the prediction of transmembrane helices in protein structures.

Jean Pylouster , Aurélie Bornot , Catherine Etchebest , Alexandre de Brevern
Amino Acids, 2010, 39 (5), pp.1241-54. ⟨10.1007/s00726-010-0559-6⟩
Article dans une revue inserm-00472869v1
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Observer avec un nouvel oeil la structure des protéines et leur flexibilité.

Alexandre de Brevern
Regard sur la biochimie, 2010, 2010 (4), pp.3
Article dans une revue inserm-00557286v1
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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
Cellular and Molecular Life Sciences, 2010, 67 (19), pp.3371-87. ⟨10.1007/s00018-010-0387-6⟩
Article dans une revue inserm-00512838v1
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Comparative analysis of missing value imputation methods to improve clustering and interpretation of microarray experiments.

Magalie Celton , Alain Malpertuy , Gaëlle Lelandais , Alexandre de Brevern
BMC Genomics, 2010, 11 (1), pp.15. ⟨10.1186/1471-2164-11-15⟩
Article dans une revue inserm-00663912v1
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A new prediction strategy for long local protein structures using an original description.

Aurélie Bornot , Catherine Etchebest , Alexandre de Brevern
Proteins - Structure, Function and Bioinformatics, 2009, 76 (3), pp.570-87. ⟨10.1002/prot.22370⟩
Article dans une revue inserm-00348740v1
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Protein short loop prediction in terms of a structural alphabet.

Manoj Tyagi , Aurélie Bornot , Bernard Offmann , Alexandre de Brevern
Computational Biology and Chemistry, 2009, 33 (4), pp.329-33. ⟨10.1016/j.compbiolchem.2009.06.002⟩
Article dans une revue inserm-00396485v1
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Editorial for Infectious Diseases - Drug Targets (in silico issue)

Alexandre de Brevern
Infectious disorders drug targets, 2009, 9 (3), pp.246-7
Article dans une revue inserm-00395256v1
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Analyzing the sequence-structure relationship of a library of local structural prototypes.

Cristina Benros , Alexandre de Brevern , Serge A. Hazout
Journal of Theoretical Biology, 2009, 256 (2), pp.215-26. ⟨10.1016/j.jtbi.2008.08.032⟩
Article dans une revue inserm-00318954v1
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Analysis of HSP90-related folds with MED-SuMo classification approach.

Olivia Doppelt-Azeroual , Fabrice Moriaud , François Delfaud , Alexandre de Brevern
Drug Design, Development and Therapy, 2009, 3, pp.59-72
Article dans une revue inserm-00348737v1
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Analysis of protein contacts into Protein Units.

Guilhem Faure , Aurélie Bornot , Alexandre de Brevern
Biochimie, 2009, 91 (7), pp.876-87. ⟨10.1016/j.biochi.2009.04.008⟩
Article dans une revue inserm-00375095v1
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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
Journal of Computer-Aided Molecular Design, 2009, 23 (8), pp.571-82. ⟨10.1007/s10822-009-9286-z⟩
Article dans une revue inserm-00396557v1
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Analysis of loop boundaries using different local structure assignment methods.

Manoj Tyagi , Aurélie Bornot , Bernard Offmann , Alexandre de Brevern
Protein Science, 2009, 18 (9), pp.1869-81. ⟨10.1002/pro.198⟩
Article dans une revue inserm-00392504v1
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Analysis of protein chameleon sequence characteristics.

Amine Ghozlane , Agnel Joseph , Aurélie Bornot , Alexandre de Brevern
Bioinformation, 2009, 3 (9), pp.367-9
Article dans une revue inserm-00353122v1
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In Silico Studies on DARC.

Alexandre de Brevern , Ludovic Autin , Yves Colin , Olivier Bertrand , Catherine Etchebest
Infectious disorders drug targets, 2009, 9 (3), pp.289-303
Article dans une revue inserm-00366309v1
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Protein contacts, inter-residue interactions and side-chain modelling.

Guilhem Faure , Aurélie Bornot , Alexandre de Brevern
Biochimie, 2008, 90 (4), pp.626-39. ⟨10.1016/j.biochi.2007.11.007⟩
Article dans une revue inserm-00189828v1
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In silico local structure approach: A case study on Outer Membrane Proteins.

Juliette Martin , Alexandre de Brevern , Anne-Claude Camproux
Proteins - Structure, Function and Bioinformatics, 2008, 71 (1), pp.92-109. ⟨10.1002/prot.21659⟩
Article dans une revue inserm-00176452v1
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A reduced amino acid alphabet for understanding and designing protein adaptation to mutation.

Catherine Etchebest , Cristina Benros , Aurélie Bornot , Anne-Claude Camproux , Alexandre de Brevern
European Biophysics Journal, 2007, 36 (8), pp.1059-69. ⟨10.1007/s00249-007-0188-5⟩
Article dans une revue inserm-00155390v1
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Protein structure mining using a structural alphabet.

Manoj Tyagi , Alexandre de Brevern , Narayanaswamy Srinivasan , Bernard Offmann
Proteins - Structure, Function and Bioinformatics, 2007, 71 (2), pp.920-937. ⟨10.1002/prot.21776⟩
Article dans une revue inserm-00176443v1
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"Pinning strategy": a novel approach for predicting the backbone structure in terms of protein blocks from sequence.

Alexandre de Brevern , Catherine Etchebest , Cristina Benros , Serge A. Hazout
Journal of Biosciences, 2007, 32 (1), pp.51-70
Article dans une revue inserm-00143368v1
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How flexible protein structures are? New questions on the protein structure plasticity.

Aurélie Bornot , Bernard Offmann , Alexandre de Brevern
BioForum Europe, 2007, 11, pp.24
Article dans une revue inserm-00189079v1
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Functional annotation strategy for protein structures

Olivia Doppelt , Fabrice Moriaud , Aurélie Bornot , Alexandre de Brevern
Bioinformation, 2007, 1 (9), pp.357-359
Article dans une revue inserm-00143366v1
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Local Protein Structures

Bernard Offmann , Manoj Tyagi , Alexandre de Brevern
Current Bioinformatics, 2007, 2, pp.165-202
Article dans une revue inserm-00175058v1
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Assessing a novel approach for predicting local 3D protein structures from sequence.

Cristina Benros , Alexandre de Brevern , Catherine Etchebest , Serge A. Hazout
Proteins - Structure, Function and Bioinformatics, 2006, 62 (4), pp.865-80. ⟨10.1002/prot.20815⟩
Article dans une revue inserm-00133180v1
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Protein Peeling 2: a web server to convert protein structures into series of protein units.

Jean-Christophe Gelly , Catherine Etchebest , Serge A. Hazout , Alexandre de Brevern
Nucleic Acids Research, 2006, 34 (Web Server issue), pp.W75-8. ⟨10.1093/nar/gkl292⟩
Article dans une revue inserm-00133731v1
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A substitution matrix for structural alphabet based on structural alignment of homologous proteins and its applications.

Manoj Tyagi , Venkataraman S. Gowri , Narayanaswamy Srinivasan , Alexandre de Brevern , Bernard Offmann
Proteins - Structure, Function and Bioinformatics, 2006, 65 (1), pp.32-9. ⟨10.1002/prot.21087⟩
Article dans une revue inserm-00133760v1
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Protein Block Expert (PBE): a web-based protein structure analysis server using a structural alphabet.

Manoj Tyagi , Priyanka Sharma , C. S. Swamy , Frédéric Cadet , N. Srinivasan
Nucleic Acids Research, 2006, 34 (Web Server issue), pp.W119-23. ⟨10.1093/nar/gkl199⟩
Article dans une revue inserm-00133751v1
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Protein beta-turn assignments.

Aurélie Bornot , Alexandre de Brevern
Bioinformation, 2006, 1 (5), pp.153-5
Article dans une revue inserm-00133658v1
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'Protein Peeling': an approach for splitting a 3D protein structure into compact fragments.

Jean-Christophe Gelly , Alexandre de Brevern , Serge A. Hazout
Bioinformatics, 2006, 22 (2), pp.129-33. ⟨10.1093/bioinformatics/bti773⟩
Article dans une revue inserm-00133725v1
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Protein secondary structure assignment revisited: a detailed analysis of different assignment methods.

Juliette Martin , Guillaume Letellier , Antoine Marin , Jean-François Taly , Alexandre de Brevern
BMC Structural Biology, 2005, 5 (17), pp.17. ⟨10.1186/1472-6807-5-17⟩
Article dans une revue inserm-00090199v1
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New assessment of a structural alphabet.

Alexandre de Brevern
In Silico Biol, 2005, 5 (3), pp.283-9
Article dans une revue inserm-00132875v1
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A structural model of a seven-transmembrane helix receptor: the Duffy antigen/receptor for chemokine (DARC).

Alexandre de Brevern , H. Wong , Christophe Tournamille , Yves Colin , Caroline Le van Kim
BBA - Biochimica et Biophysica Acta, 2005, 1724 (3), pp.288-306. ⟨10.1016/j.bbagen.2005.05.016⟩
Article dans une revue inserm-00143373v1
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A structural alphabet for local protein structures: improved prediction methods.

Catherine Etchebest , Cristina Benros , Serge A. Hazout , Alexandre de Brevern
Proteins - Structure, Function and Bioinformatics, 2005, 59 (4), pp.810-27. ⟨10.1002/prot.20458⟩
Article dans une revue inserm-00143564v1
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Local backbone structure prediction of proteins.

Alexandre de Brevern , Cristina Benros , Romain Gautier , Hélène Valadié , Serge A. Hazout
In Silico Biol, 2004, 4 (3), pp.381-6
Article dans une revue inserm-00132872v1
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Use of a structural alphabet for analysis of short loops connecting repetitive structures.

Laurent Fourrier , Cristina Benros , Alexandre de Brevern
BMC Bioinformatics, 2004, 5, pp.58. ⟨10.1186/1471-2105-5-58⟩
Article dans une revue inserm-00112104v1
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Influence of microarrays experiments missing values on the stability of gene groups by hierarchical clustering.

Alexandre de Brevern , Serge A. Hazout , Alain Malpertuy
BMC Bioinformatics, 2004, 5, pp.114. ⟨10.1186/1471-2105-5-114⟩
Article dans une revue inserm-00000113v1
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'Hybrid protein model' for optimally defining 3D protein structure fragments.

Alexandre de Brevern , Serge A. Hazout
Bioinformatics, 2003, 19 (3), pp.345-53. ⟨10.1093/bioinformatics/btf859⟩
Article dans une revue inserm-00133632v1
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Genome compartimentation by a hybrid chromosome model (HXM). Application to Saccharomyces cerevisae subtelomeres

Alexandre de Brevern , France Loirat , Anne Badel-Chagnon , Cécile André , Pierre Vincens
Comput Chem, 2002, 26 (5), pp.437-45. ⟨10.1016/S0097-8485(02)00006-2⟩
Article dans une revue inserm-00143383v1
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Compartimentation chromosomique

Alexandre de Brevern
Biofutur, 2002, 225, pp.20-22
Article dans une revue inserm-00132826v1
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Extension of a local backbone description using a structural alphabet: a new approach to the sequence-structure relationship.

Alexandre de Brevern , Hélène Valadié , Serge A. Hazout , Catherine Etchebest
Protein Science, 2002, 11 (12), pp.2871-86
Article dans une revue inserm-00143374v1
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Compacting local protein folds with a Hybrid Protein

Alexandre de Brevern , Serge A. Hazout
Theoretical Chemistry Accounts: Theory, Computation, and Modeling, 2001, 106 (1/2), pp.36-47. ⟨10.1007/s002140000227⟩
Article dans une revue inserm-00132867v1
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Exploring the use of a structural alphabet for a structural prediction of protein loops

Anne-Claude Camproux , Alexandre de Brevern , Serge A. Hazout , Pierre Tufféry
Theoretical Chemistry Accounts: Theory, Computation, and Modeling, 2001, 106 (1/2), pp.28-35. ⟨10.1007/s002140100261⟩
Article dans une revue inserm-00134555v1
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Bayesian probabilistic approach for predicting backbone structures in terms of protein blocks.

Alexandre de Brevern , Catherine Etchebest , Serge A. Hazout
Proteins - Structure, Function and Bioinformatics, 2000, 41 (3), pp.271-87
Article dans une revue inserm-00132821v1
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Analysis of allosteric effect of pathologic variants at the light of local protein conformations

Alexandre de Brevern
Belgrade BioInformatics Conference – BelBi 2018, Jun 2018, Belgrade, Serbia
Communication dans un congrès inserm-01853665v1
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Protein structure analysis, prediction and flexibility in the light of a structural alphabet

Alexandre de Brevern
1ère réunion du GT MASIM du GDR BIM, GDR BIM (CNRS), Nov 2017, Paris, France
Communication dans un congrès inserm-01636581v1
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Dynamics and deformability of α-, 310- and π-helices

Nicolas Shinada , Tarun Jairaj Narwani , Pierrick Craveur , Hubert Santuz , Joseph Rebehmed
20e congrès du GGMM (groupe de graphisme et modélisation moléculaire), May 2017, Reims, France
Communication dans un congrès inserm-01581259v1

PB-PENTAdb : a web resource for the analysis and prediction of local backbone structure and flexibility using pentapeptide protein blocks

Bernard Offmann , M. Tyagi , A. Joseph , M. Drula , M. Grondin
9th European Congress on Computation Biology (ECCB10), Sep 2010, Ghent, Belgium
Communication dans un congrès hal-01198468v1
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Hybrid Protein Model (HPM) : A Method For Building A Library Of Overlapping Local Structural Prototypes. Sensitivity Study And Improvements Of The Training

Cristina Benros , Alexandre de Brevern , Serge Hazout
2003, pp.53-72
Communication dans un congrès inserm-00133639v1
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"Hybrid Protein Model": a new clustering approach for 3D local structures

Cristina Benros , Serge A. Hazout , Alexandre de Brevern
2002, pp.36-45
Communication dans un congrès inserm-00134559v1
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Hybrid Protein Model (HPM): a method to compact protein 3D-structures information and physicochemical properties.

Alexandre de Brevern , Serge A. Hazout
Communication dans un congrès inserm-00132863v1
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"Hybrid Protein Model (HPM)" : une nouvelle approche pour caractériser les relations séquence-structure dans les protéines

Alexandre de Brevern , Serge A. Hazout
2000, pp.105-112
Communication dans un congrès inserm-00134567v1
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Analyse par dynamiques moléculaires de 5 types de Calréticuline associée à la thrombocytémie essentielle

Ragousandirane Radjasandirane , Alexandre de Brevern
43e congrès de la Société Française d'Hématologie, Mar 2024, Paris, France
Poster de conférence inserm-04072440v1
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Evaluation of 50 Computational Tools for Predicting Pathogenicity of Genetic Variants: Unveiling representativeness issues on public datasets

Ragousandirane Radjasandirane , Jean-Christophe Gelly , Julien Diharce , Alexandre de Brevern
International Symposium on Human Genomics, Sep 2023, Paris, France
Poster de conférence hal-04264309v1
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Analysis of VHH dynamics

Akhila Melarkode Vattekatte , Julien Diharce , Catherine Etchebest , Alexandre de Brevern
67th Biophysical Society Annual Meeting, Feb 2023, San Diego (California), United States
Poster de conférence inserm-04072706v1
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On the turning away

Alexandre de Brevern
Joint 25th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) and 16th European Conference on Computational Biology (ECCB) 2017, Aug 2017, Prague, Czech Republic. , 2017
Poster de conférence inserm-01575565v1
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Comparative Analysis of Protein -Protein Interface Methods

Alexandre de Brevern , Jérémy Esque
Groupe Graphisme Modélisation Moléculaire (GGMM), May 2017, Reims, France
Poster de conférence inserm-01586501v1

On the turning away

Alexandre de Brevern
20e congrès du GGMM (groupe de graphisme et modélisation moléculaire), Aug 2017, Reims, France. 2017
Poster de conférence inserm-01575727v1

Bioinformatique - 3e édition

Gilbert Deléage , Manolo Gouy , Alexandre de Brevern
Dunod, 2021, Collection Sciences Sup, 978-2-10-081515-9
Ouvrages hal-03356596v1
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A bioinformatic web server to cut protein structures in terms of Protein Units.

Jean-Christophe Gelly , Alexandre de Brevern
Jaclyn E. Morris. Computer Science Research and the Internet, Nova Book Press, pp.169-183, 2011
Chapitre d'ouvrage inserm-00646177v1

Modélisation des systèmes biologiques, bioinformatique

Olivier Gascuel , P. Benas , C. Brun , D. Burnouf , Alexandre de Brevern
Rapport de conjoncture 2010 du Comité national de la recherche scientifique, CNRS Editions, chapitre 43, 845-858, 2011, 978-2-271-07263-4
Chapitre d'ouvrage hal-00799641v1
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Characterization of Conformational Patterns in Active and Inactive Forms of Kinases Using Protein Blocks Approach.

Garima Agarwal , Dhurvas Chandrasekaran Dinesh , Narayanaswamy Srinivasan , Alexandre de Brevern
Ujjwal Maulik, Sanghamitra Bandyopadhyay, Jason T. L. Wang. Computational Intelligence and Pattern Analysis in Biological Informatics, Wiley, pp.169-188, 2010, ⟨10.1002/9780470872352.ch8⟩
Chapitre d'ouvrage inserm-00557296v1
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Local Structure Alphabets

Agnel Joseph , Aurélie Bornot , Alexandre de Brevern
Huzefa Rangwala, George Karypis. Introduction to Protein Structure Prediction: Methods and Algorithms, Wiley, pp.75-106, 2010, ⟨10.1002/9780470882207.ch5⟩
Chapitre d'ouvrage inserm-00557300v1
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Description of the local protein structure. I. Classical approaches.

Cristina Benros , Juliette Martin , Manoj Tyagi , Alexandre de Brevern
Alexandre G. de Brevern. Recent Advances in Structural Bioinformatics, Research Signpost, Trivandrum, Kerala, India., pp.6-27, 2007
Chapitre d'ouvrage inserm-00176471v1
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Description of the local protein structure. II. Novel approaches.

Manoj Tyagi , Cristina Benros , Juliette Martin , Alexandre de Brevern
Alexandre G. de Brevern. Recent Advances in Structural Bioinformatics, Research Signpost, Trivandrum, Kerala, India., pp.28-42, 2007
Chapitre d'ouvrage inserm-00176668v1
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Turns prediction

Patrick Fuchs , Catherine Etchebest , Alexandre de Brevern
Alexandre G. de Brevern. Recent Advances in Structural Bioinformatics, Research Signpost, Trivandrum, Kerala, India., pp.43-63, 2007
Chapitre d'ouvrage inserm-00176710v1
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Structural Alphabet: From a Local Point of View to a Global Description of Protein 3D Structures

Alexandre de Brevern , Cristina Benros , Serge A. Hazout
Yan, Peter V. Bioinformatics: New Research, Nova publishers, pp.127-69, 2005
Chapitre d'ouvrage inserm-00134564v1
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Protein structural alphabets: beyond the secondary structure description

Alexandre de Brevern , Anne-Claude Camproux , Serge A. Hazout , Catherine Etchebest , Pierre Tufféry
Sangadai SG. Recent research developments in protein engineering, Research signpost, pp.319-331, 2001
Chapitre d'ouvrage inserm-00133650v1