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Number of documents

142

Alexandre de Brevern CV


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Journal articles120 documents

  • Sali Anies, Vincent Jallu, Julien Diharce, Tarun J Narwani, Alexandre G de Brevern. Analysis of Integrin αIIb Subunit Dynamics Reveals Long-Range Effects of Missense Mutations on Calf Domains. International Journal of Molecular Sciences, MDPI, 2022, 23 (2), pp.858. ⟨10.3390/ijms23020858⟩. ⟨hal-03542900⟩
  • Nora El Jahrani, Gabriel Cretin, Alexandre de Brevern. CALR-ETdb, the database of calreticulin variants diversity in essential thrombocythemia. Platelets, Taylor & Francis, 2022, 33 (1), pp.157-167. ⟨10.1080/09537104.2020.1869712⟩. ⟨hal-03695851⟩
  • M Koker, N Sarper, C Albayrak, B Zulfikar, E Zengin, et al.. New αIIbβ3 variants in 28 Turkish Glanzmann patients; structural hypothesis for complex activation by residues variations in I-EGF domains. Platelets, Taylor & Francis, 2022, 33 (4), pp.551-561. ⟨10.1080/09537104.2021.1947481⟩. ⟨hal-03684658⟩
  • Poonam Vishwakarma, Akhila Melarkode Vattekatte, Nicolas Shinada, Julien Diharce, Carla Martins, et al.. VHH Structural Modelling Approaches: A Critical Review. International Journal of Molecular Sciences, MDPI, 2022, 23 (7), pp.3721. ⟨10.3390/ijms23073721⟩. ⟨hal-03665842⟩
  • Gabriel Cretin, Tatiana Galochkina, Yann Vander Meersche, Alexandre G de Brevern, Guillaume Postic, et al.. SWORD2: hierarchical analysis of protein 3D structures. Nucleic Acids Research, Oxford University Press, 2022, 50 (W1), pp.W732--W738. ⟨10.1093/nar/gkac370⟩. ⟨hal-03738483⟩
  • Mirjana Maljković, Nenad Mitić, Alexandre de Brevern. Prediction of structural alphabet protein blocks using data mining. Biochimie, 2022, 197, pp.74-85. ⟨10.1016/j.biochi.2022.01.019⟩. ⟨hal-03652564⟩
  • Alexandre de Brevern, Joseph Rebehmed. Current status of PTMs structural databases: applications, limitations and prospects. Amino Acids, Springer Verlag, 2022, 54 (4), pp.575-590. ⟨10.1007/s00726-021-03119-z⟩. ⟨hal-03690712⟩
  • Aline Floch, Stéphane Téletchéa, Christophe Tournamille, Alexandre de Brevern, France Pirenne. A Review of the Literature Organized Into a New Database: RHeference. Transfusion Medicine Reviews, WB Saunders, 2021, 35 (2), pp.70-77. ⟨10.1016/j.tmrv.2021.04.002⟩. ⟨inserm-03253477⟩
  • Ralfs Buks, Mégane Brusson, Sylvie Cochet, Tatiana Galochkina, Bruno Cassinat, et al.. ABCG2 Is Overexpressed on Red Blood Cells in Ph-Negative Myeloproliferative Neoplasms and Potentiates Ruxolitinib-Induced Apoptosis. International Journal of Molecular Sciences, MDPI, 2021, 22 (7), pp.3530. ⟨10.3390/ijms22073530⟩. ⟨hal-03531056⟩
  • Akhila Melarkode Vattekatte, Frédéric Cadet, Jean-Christophe Gelly, Alexandre de Brevern. Insights into Comparative Modeling of VHH Domains. International Journal of Molecular Sciences, MDPI, 2021, 22 (18), pp.9771. ⟨10.3390/ijms22189771⟩. ⟨hal-03537422⟩
  • Jade Fogha, Jagadeesh Bayry, Julien Diharce, Alexandre de Brevern. Structural and evolutionary exploration of the IL-3 family and its alpha subunit receptors. Amino Acids, Springer Verlag, 2021, 53 (8), pp.1211-1227. ⟨10.1007/s00726-021-03026-3⟩. ⟨hal-03538521⟩
  • Aline Floch, France Pirenne, Aurélie Barrault, Btissam Chami, Cécile Toly‐ndour, et al.. Insights into anti‐D formation in carriers of RhD variants through studies of 3D intraprotein interactions. Transfusion, Wiley, 2021, 61 (4), pp.1286-1301. ⟨10.1111/trf.16301⟩. ⟨inserm-03253510⟩
  • Himani Tandon, Alexandre de Brevern, Narayanaswamy Srinivasan. Transient association between proteins elicits alteration of dynamics at sites far away from interfaces. Structure, Elsevier (Cell Press), 2021, 29 (4), pp.371-384.e3. ⟨10.1016/j.str.2020.11.015⟩. ⟨inserm-03543689⟩
  • Ashraya Ravikumar, Alexandre de Brevern, Narayanaswamy Srinivasan. Conformational Strain Indicated by Ramachandran Angles for the Protein Backbone Is Only Weakly Related to the Flexibility. Journal of Physical Chemistry B, American Chemical Society, 2021, 125 (10), pp.2597-2606. ⟨10.1021/acs.jpcb.1c00168⟩. ⟨hal-03549944⟩
  • Alexei Nekrasov, Yuri Kozmin, Sergey Kozyrev, Rustam Ziganshin, Alexandre de Brevern, et al.. Hierarchical Structure of Protein Sequence. International Journal of Molecular Sciences, MDPI, 2021, 22 (15), pp.8339. ⟨10.3390/ijms22158339⟩. ⟨hal-03538152⟩
  • Akhila Melarkode Vattekatte, Tarun Jairaj Narwani, Aline Floch, Mirjana Maljković, Soubika Bisoo, et al.. Data set of intrinsically disordered proteins analysed at a local protein conformation level. Data in Brief, Elsevier, 2020, 29, pp.105383. ⟨10.1016/j.dib.2020.105383⟩. ⟨hal-02935063⟩
  • Akhila Melarkode Vattekatte, Tarun Jairaj Narwani, Aline Floch, Mirjana Maljković, Soubika Bisoo, et al.. Data set of intrinsically disordered proteins analysed at a local protein conformation level. Data in Brief, Elsevier, 2020, 29, pp.105383. ⟨10.1016/j.dib.2020.105383⟩. ⟨inserm-02907359⟩
  • Nicolas K Shinada, Peter Schmidtke, Alexandre de Brevern. Accurate Representation of Protein-Ligand Structural Diversity in the Protein Data Bank (PDB). International Journal of Molecular Sciences, MDPI, 2020, 21 (6), pp.2243. ⟨10.3390/ijms21062243⟩. ⟨inserm-02907370⟩
  • Alexandre de Brevern. Analysis of Protein Disorder Predictions in the Light of a Protein Structural Alphabet. Biomolecules, MDPI, 2020, 10 (7), pp.1080. ⟨10.3390/biom10071080⟩. ⟨inserm-02907391⟩
  • Akhila Melarkode Vattekatte, Nicolas Ken Shinada, Tarun J Narwani, Floriane Noël, Olivier Bertrand, et al.. Discrete analysis of camelid variable domains: sequences, structures, and in-silico structure prediction: Sequence-structure characteristics of VHH domains. PeerJ, PeerJ, 2020, 8, pp.e8408. ⟨10.7717/peerj.8408⟩. ⟨inserm-02907323⟩
  • Akhila Melarkode Vattekatte, Tarun Jairaj Narwani, Aline Floch, Mirjana Maljković, Soubika Bisoo, et al.. A structural entropy index to analyse local conformations in intrinsically disordered proteins: IDP PBs. Journal of Structural Biology, Elsevier, 2020, 210 (1), pp.107464. ⟨10.1016/j.jsb.2020.107464⟩. ⟨inserm-02907335⟩
  • Andrea Hill, Salwa Karboune, Tarun Narwani, Alexandre de Brevern. Investigating the Product Profiles and Structural Relationships of New Levansucrases with Conventional and Non-Conventional Substrates. International Journal of Molecular Sciences, MDPI, 2020, 21 (15), pp.5402. ⟨10.3390/ijms21155402⟩. ⟨inserm-02913693⟩
  • Anna Guadall, Sylvie Cochet, Olivier Renaud, Yves Colin, Caroline Le van Kim, et al.. Dimerization and phosphorylation of Lutheran/basal cell adhesion molecule are critical for its function in cell migration on laminin. Journal of Biological Chemistry, American Society for Biochemistry and Molecular Biology, 2019, 294 (41), pp.14911-14921. ⟨10.1074/jbc.RA119.007521⟩. ⟨hal-02416861⟩
  • R. Kalaivani, T. J Narwani, Alexandre de Brevern, N. Srinivasan. Long-range molecular dynamics show that inactive forms of Protein Kinase A are more dynamic than active forms. Protein Science, Wiley, 2019, 28 (3), pp.543-560. ⟨10.1002/pro.3556⟩. ⟨inserm-02913871⟩
  • Akhila Melarkode Vattekatte, Tarun Jairaj Narwani, Pierrick Craveur, Nicolas K Shinada, Aline Floch, et al.. Discrete analyses of protein dynamics. Journal of Biomolecular Structure and Dynamics, Taylor & Francis: STM, Behavioural Science and Public Health Titles, 2019, pp.1-15. ⟨10.1080/07391102.2019.1650112⟩. ⟨inserm-02266159⟩
  • Etienne Ruppé, Amine Ghozlane, Julien Tap, Nicolas Pons, Anne-Sophie Alvarez, et al.. Prediction of the intestinal resistome by a three-dimensional structure-based method. Nature Microbiology, Nature Publishing Group, 2019, 4 (1), pp.112-123. ⟨10.1038/s41564-018-0292-6⟩. ⟨pasteur-02552015⟩
  • Guilhem Faure, Agnel Praveen Joseph, Pierrick Craveur, Tarun Narwani, Narayanaswamy Srinivasan, et al.. iPBAvizu: a PyMOL plugin for an efficient 3D protein structure superimposition approach. Source Code for Biology and Medicine, BioMed Central, 2019, 14 (1), ⟨10.1186/s13029-019-0075-3⟩. ⟨inserm-02913723⟩
  • Alexei N Nekrasov, Ludmila G Alekseeva, Rudolf А. Pogosyan, Dmitry A Dolgikh, M.P. P Kirpichnikov, et al.. A minimum set of stable blocks for rational design of polypeptide chains Running head: A set of stable blocks for protein rational design. Biochimie, Elsevier, 2019, 160, pp.88-92. ⟨10.1016/j.biochi.2019.02.006⟩. ⟨inserm-02266188⟩
  • Pierrick Craveur, Tarun Narwani, Joseph Rebehmed, Alexandre de Brevern. Investigation of the impact of PTMs on the protein backbone conformation. Amino Acids, Springer Verlag, 2019, 51 (7), pp.1065-1079. ⟨10.1007/s00726-019-02747-w⟩. ⟨inserm-02266176⟩
  • Henri Wajcman, Alexandre de Brevern, Jean Riou, Céline Latouche, Michael C. Marden, et al.. 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. Hemoglobin, Informa Healthcare, 2019, 42 (5-6), pp.287-293. ⟨10.1080/03630269.2018.1556683⟩. ⟨inserm-02913864⟩
  • Nicolas Shinada, Alexandre de Brevern, Peter Schmidtke. Halogens in Protein−Ligand Binding Mechanism: A Structural Perspective. Journal of Medicinal Chemistry, American Chemical Society, 2019, 62 (21), pp.9341-9356. ⟨10.1021/acs.jmedchem.8b01453⟩. ⟨inserm-02913756⟩
  • Iyanar Vetrivel, Alexandre de Brevern, Frédéric Cadet, Narayanaswamy Srinivasan, Bernard Offmann. Structural variations within proteins can be as large as variations observed across their homologues. Biochimie, Elsevier, 2019, 167, pp.162-170. ⟨10.1016/j.biochi.2019.09.013⟩. ⟨inserm-02913845⟩
  • Tarun J. Narwani, Catherine Etchebest, Pierrick Craveur, Sylvain Léonard, Joseph Rebehmed, et al.. In silico prediction of protein flexibility with local structure approach. Biochimie, Elsevier, 2019, 165, pp.150-155. ⟨10.1016/j.biochi.2019.07.025⟩. ⟨inserm-02266143⟩
  • Vincent Demolombe, Alexandre de Brevern, Liza L. Felicori, Christophe Nguyen, Ricardo Andrez Machado de Avila, et al.. PEPOP 2.0: new approaches to mimic non-continuous epitopes. BMC Bioinformatics, BioMed Central, 2019, 20 (1), ⟨10.1186/s12859-019-2867-5⟩. ⟨hal-02277257⟩
  • Vincent Demolombe, Alexandre de Brevern, Franck Molina, Géraldine Lavigne, Claude Granier, et al.. Benchmarking the PEPOP methods for mimicking discontinuous epitopes. BMC Bioinformatics, BioMed Central, 2019, 20 (1), pp.738. ⟨10.1186/s12859-019-3189-3⟩. ⟨hal-02787607v2⟩
  • Tarun Narwani, Pierrick Craveur, Nicolas Shinada, Hubert Santuz, Joseph Rebehmed, et al.. Dynamics and deformability of α-, 310- and π-helices. Archives of Biological Science, Srpsko Biološko Društvo, 2018, 70 (1), pp.21-31. ⟨10.2298/ABS170215022N⟩. ⟨inserm-01585114⟩
  • Sneha Vishwanath, Alexandre de Brevern, Narayanaswamy Srinivasan. Same but not alike: Structure, flexibility and energetics of domains in multi-domain proteins are influenced by the presence of other domains. PLoS Computational Biology, Public Library of Science, 2018, 14 (2), pp.e1006008. ⟨10.1371/journal.pcbi.1006008⟩. ⟨inserm-02147944⟩
  • Alexandre de Brevern. Analysing the Structural Effect of Point Mutations of Cytotoxic Necrotizing Factor 1 (CNF1) on Lu/BCAM Adhesion Glycoprotein Association. Toxins, MDPI, 2018, 10 (3), pp.E122. ⟨10.3390/toxins10030122⟩. ⟨inserm-01852766⟩
  • Alexandre de Brevern. Protein local conformations at the light of a structural alphabet. Biophysical Journal, Biophysical Society, 2018, 114 (3), pp.231A. ⟨10.1016/j.bpj.2017.11.1286⟩. ⟨inserm-01852960⟩
  • Iyanar Vetrivel, Swapnil Mahajan, Manoj Tyagi, Lionel Hoffmann, Yves-Henri Sanejouand, et al.. Knowledge-based prediction of protein backbone conformation using a structural alphabet. PLoS ONE, Public Library of Science, 2017, 12 (11), pp.e0186215. ⟨10.1371/journal.pone.0186215⟩. ⟨hal-01677391⟩
  • Aline Floch, Aurelie Barrault, Alexandre de Brevern, Jennifer Martret, Kevin Gaillard, et al.. Molecular characterization of 13 new RHD alleles. Transfusion, Wiley, 2017, 57 (4), pp. 1089-1091. ⟨10.1111/trf.14004⟩. ⟨hal-01627823⟩
  • Tarun Jairaj Narwani, Hubert Santuz, Nicolas Shinada, Akhila Melarkode Vattekatte, Yassine Ghouzam, et al.. Recent advances on polyproline II.. Amino Acids, Springer Verlag, 2017, 49 (4), pp.705-713. ⟨10.1007/s00726-017-2385-6⟩. ⟨inserm-01573940⟩
  • Alexandre de Brevern. Extension of the classical classification of β-turns: new turns. Scientific Reports, Nature Publishing Group, 2016, pp.33191 ⟨10.1038/srep33191⟩. ⟨inserm-01374651⟩
  • Swapnil Mahajan, Alexandre de Brevern, Yves-Henri Sanejouand, Narayanaswamy Srinivasan, Bernard Offmann. Use of a structural alphabet to find compatible folds for amino acid sequences. Protein Science, Wiley, 2015, 24 (1), pp.145 - 153. ⟨10.1002/pro.2581⟩. ⟨hal-01677393⟩
  • Sylvain Léonard, Agnel Praveen Joseph, Narayanaswamy Srinivasan, Jean-Christophe Gelly, Alexandre de Brevern. mulPBA: an efficient multiple protein structure alignment method based on a structural alphabet.. Journal of Biomolecular Structure and Dynamics, Taylor & Francis: STM, Behavioural Science and Public Health Titles, 2014, 32 (4), pp.661-8. ⟨10.1080/07391102.2013.787026⟩. ⟨inserm-00926338⟩
  • Swapnil Mahajan, Alexandre de Brevern, Bernard Offmann, Narayanaswamy Srinivasan. Correlation between local structural dynamics of proteins inferred from NMR ensembles and evolutionary dynamics of homologues of known structure.: Inherent and evolutionary structural dynamics. Journal of Biomolecular Structure and Dynamics, Taylor & Francis: STM, Behavioural Science and Public Health Titles, 2014, 32 (5), pp.751-8. ⟨10.1080/07391102.2013.789989⟩. ⟨inserm-00926204⟩
  • Bohdan Schneider, Jirí Cerny, Daniel Svozil, Petr Cech, Jean-Christophe Gelly, et al.. Bioinformatic analysis of the protein/DNA interface.. Nucleic Acids Research, Oxford University Press, 2014, 42 (5), pp.3381-94. ⟨10.1093/nar/gkt1273⟩. ⟨inserm-00926088⟩
  • Pierrick Craveur, Agnel Praveen Joseph, Joseph Rebehmed, Alexandre de Brevern. β-Bulges: extensive structural analyses of β-sheets irregularities.. Protein Science, Wiley, 2013, 22 (10), pp.1366-78. ⟨10.1002/pro.2324⟩. ⟨inserm-00926388⟩
  • Joseph Rebehmed, Véronique Alphand, Véronique de Berardinis, Alexandre de Brevern. Evolution study of the Baeyer-Villiger monooxygenases enzyme family: functional importance of the highly conserved residues.. Biochimie, Elsevier, 2013, 95 (7), pp.1394-402. ⟨10.1016/j.biochi.2013.03.005⟩. ⟨inserm-00926584⟩
  • Swapnil Mahajan, Garima Agarwal, Mohammed Iftekhar, Bernard Offmann, Alexandre de Brevern, et al.. DoSA: Database of Structural Alignments.. Database - The journal of Biological Databases and Curation, Oxford University Press, 2013, 2013, pp.bat048. ⟨10.1093/database/bat048⟩. ⟨inserm-00926452⟩
  • Ramachandra M Bhaskara, Alexandre de Brevern, Narayanaswamy Srinivasan. Understanding the role of domain-domain linkers in the spatial orientation of domains in multi-domain proteins.. Journal of Biomolecular Structure and Dynamics, Taylor & Francis: STM, Behavioural Science and Public Health Titles, 2013, 31 (12), pp.1467-80. ⟨10.1080/07391102.2012.743438⟩. ⟨inserm-00926595⟩
  • Lucie Chevrier, Alexandre de Brevern, Eva Hernandez, Jérome Leprince, Hubert Vaudry, et al.. PRR repeats in the intracellular domain of KISS1R are important for its export to cell membrane.: PRR repeats in intracellular domain of KISSIR. Mol Endocrinol, 2013, 27 (6), pp.1004-14. ⟨10.1210/me.2012-1386⟩. ⟨inserm-00926577⟩
  • Pierrick Craveur, Agnel Praveen Joseph, Pierre Poulain, Joseph Rebehmed, Alexandre de Brevern. Cis-trans isomerization of omega dihedrals in proteins.. Amino Acids, Springer Verlag, 2013, 45 (2), pp.279-89. ⟨10.1007/s00726-013-1511-3⟩. ⟨inserm-00926521⟩
  • Jérémy Esque, Sylvain Léonard, Alexandre de Brevern, Christophe Oguey. VLDP web server: a powerful geometric tool for analysing protein structures in their environment.. Nucleic Acids Research, Oxford University Press, 2013, 41 (Web Server issue), pp.W373-8. ⟨10.1093/nar/gkt509⟩. ⟨inserm-00926547⟩
  • Vincent Jallu, Pierre Poulain, Patrick F. J. Fuchs, Cécile Kaplan, Alexandre de Brevern. Modeling and molecular dynamics of HPA-1a and -1b polymorphisms: effects on the structure of the β3 subunit of the αIIbβ3 integrin.. PLoS ONE, Public Library of Science, 2012, 7 (11), pp.e47304. ⟨10.1371/journal.pone.0047304⟩. ⟨inserm-00926600⟩
  • Agnel Praveen Joseph, Hélène Valadié, Narayanaswamy Srinivasan, Alexandre de Brevern. Local structural differences in homologous proteins: specificities in different SCOP classes.. PLoS ONE, Public Library of Science, 2012, 7 (6), pp.e38805. ⟨10.1371/journal.pone.0038805⟩. ⟨inserm-00750286⟩
  • Lakshmipuram S. Swapna, Swapnil Mahajan, Alexandre de Brevern, Narayanaswamy Srinivasan. Comparison of tertiary structures of proteins in protein-protein complexes with unbound forms suggests prevalence of allostery in signalling proteins.. BMC Structural Biology, BioMed Central, 2012, 12 (1), pp.6. ⟨10.1186/1472-6807-12-6⟩. ⟨inserm-00725334⟩
  • Agnel Praveen Joseph, Narayanaswamy Srinivasan, Alexandre de Brevern. Cis-trans peptide variations in structurally similar proteins.: Conservation of omega dihedral angle. Amino Acids, Springer Verlag, 2012, 43 (3), pp.1369-81. ⟨10.1007/s00726-011-1211-9⟩. ⟨inserm-00680773⟩
  • Jean-Christophe Gelly, Hsuan-Yu Lin, Alexandre de Brevern, Trees-Juen Chuang, Feng-Chi Chen. Selective constraint on human pre-mRNA splicing by protein structural properties.. Genome Biol Evol, Oxford University Press, 2012, 4 (9), pp.966-75. ⟨10.1093/gbe/evs071⟩. ⟨inserm-00750397⟩
  • Agnel Praveen Joseph, Narayanaswamy Srinivasan, Alexandre de Brevern. Progressive structure-based alignment of homologous proteins: Adopting sequence comparison strategies.. Biochimie, Elsevier, 2012, 94 (9), pp.2025-34. ⟨10.1016/j.biochi.2012.05.028⟩. ⟨inserm-00750325⟩
  • Alexandre de Brevern, Aurélie Bornot, Pierrick Craveur, Catherine Etchebest, Jean-Christophe Gelly. PredyFlexy: flexibility and local structure prediction from sequence.. Nucleic Acids Research, Oxford University Press, 2012, 40 (Web Server issue), pp.W317-22. ⟨10.1093/nar/gks482⟩. ⟨inserm-00750270⟩
  • Garima Agarwal, Swapnil Mahajan, Narayanaswamy Srinivasan, Alexandre de Brevern. Identification of local conformational similarity in structurally variable regions of homologous proteins using protein blocks.. PLoS ONE, Public Library of Science, 2011, 6 (3), pp.e17826. ⟨10.1371/journal.pone.0017826⟩. ⟨inserm-00586691⟩
  • Aurélie Bornot, Catherine Etchebest, Alexandre de Brevern. Predicting protein flexibility through the prediction of local structures.. Proteins - Structure, Function and Bioinformatics, Wiley, 2011, 79 (3), pp.839-52. ⟨10.1002/prot.22922⟩. ⟨inserm-00568171⟩
  • Jean-Christophe Gelly, Agnel Praveen Joseph, Narayanaswamy Srinivasan, Alexandre de Brevern. iPBA: a tool for protein structure comparison using sequence alignment strategies.: Structural Alphabet Alignment. Nucleic Acids Research, Oxford University Press, 2011, 39 (Web Server issue), pp.W18-23. ⟨10.1093/nar/gkr333⟩. ⟨inserm-00646241⟩
  • Agnel Praveen Joseph, Narayanaswamy Srinivasan, Alexandre de Brevern. Improvement of protein structure comparison using a structural alphabet.. Biochimie, Elsevier, 2011, 93 (9), pp.1434-45. ⟨10.1016/j.biochi.2011.04.010⟩. ⟨inserm-00646245⟩
  • Alexandre de Brevern, Agnel Praveen Joseph, Hélène Valadié. Species specific amino acid sequence - Protein local structure relationships: An analysis in the light of a structural alphabet. Journal of Theoretical Biology, Elsevier, 2011, 276 (1), pp.209. ⟨10.1016/j.jtbi.2011.01.047⟩. ⟨hal-00682413⟩
  • Jeremy Esque, Christophe Oguey, Alexandre de Brevern. Comparative analysis of threshold and tessellation methods for determining protein contacts.. Journal of Chemical Information and Modeling, American Chemical Society, 2011, 51 (2), pp.493-507. ⟨10.1021/ci100195t⟩. ⟨inserm-00568174⟩
  • Jean-Christophe Gelly, Alexandre de Brevern. Protein Peeling 3D: new tools for analyzing protein structures.. Bioinformatics, Oxford University Press (OUP), 2011, 27 (1), pp.132-3. ⟨10.1093/bioinformatics/btq610⟩. ⟨inserm-00568165⟩
  • Yohann Mansiaux, Agnel Praveen Joseph, Jean-Christophe Gelly, Alexandre de Brevern. Assignment of PolyProline II Conformation and Analysis of Sequence - Structure Relationship.. PLoS ONE, Public Library of Science, 2011, 6 (3), pp.e18401. ⟨10.1371/journal.pone.0018401⟩. ⟨inserm-00586725⟩
  • Anabelle Amiard, Céline Baczynski, Christophe Blanchet, Alexandre de Brevern, Emmanuelle Dorlanne-Messiaen, et al.. Le cahier de laboratoire électronique (CLE). STP Pharma Pratiques, 2011, 21 (6), pp.475-503. ⟨inserm-00680791⟩
  • Alexandre de Brevern, Agnel Praveen Joseph. Species specific amino acid sequence-protein local structure relationships: An analysis in the light of a structural alphabet.: species‟ sequence - structure relationship. Journal of Theoretical Biology, Elsevier, 2011, 276 (1), pp.209-17. ⟨10.1016/j.jtbi.2011.01.047⟩. ⟨inserm-00646218⟩
  • Dorota Smolarek, Claude Hattab, Gholamreza Hassanzadeh-Ghassabeh, Sylvie Cochet, Carlos Gutiérrez, et al.. A recombinant dromedary antibody fragment (VHH or nanobody) directed against human Duffy antigen receptor for chemokines.. Cellular and Molecular Life Sciences, Springer Verlag, 2010, 67 (19), pp.3371-87. ⟨10.1007/s00018-010-0387-6⟩. ⟨inserm-00512838⟩
  • Magalie Celton, Alain Malpertuy, Gaëlle Lelandais, Alexandre de Brevern. Comparative analysis of missing value imputation methods to improve clustering and interpretation of microarray experiments.. BMC Genomics, BioMed Central, 2010, 11 (1), pp.15. ⟨10.1186/1471-2164-11-15⟩. ⟨inserm-00663912⟩
  • Jeremy Esque, Christophe Oguey, Alexandre de Brevern. A novel evaluation of residue and protein volumes by means of Laguerre tessellation.. Journal of Chemical Information and Modeling, American Chemical Society, 2010, 50 (5), pp.947-60. ⟨10.1021/ci9004892⟩. ⟨inserm-00473943⟩
  • Agnel Joseph, Garima Agarwal, Swapnil Mahajan, Jean-Christophe Gelly, Lakshmipuram S. Swapna, et al.. A short survey on protein blocks.. Biophysical Reviews, 2010, 2 (3), pp.137-147. ⟨10.1007/s12551-010-0036-1⟩. ⟨inserm-00512823⟩
  • Lionel Arnaud, Carole Saison, Virginie Helias, Nicole Lucien, Dominique Steschenko, et al.. A dominant mutation in the gene encoding the erythroid transcription factor KLF1 causes a congenital dyserythropoietic anemia.. American Journal of Human Genetics, Elsevier (Cell Press), 2010, 87 (5), pp.721-7. ⟨10.1016/j.ajhg.2010.10.010⟩. ⟨inserm-00550723⟩
  • Dorota Smolarek, Olivier Bertrand, Marcin Czerwinski, Yves Colin, Catherine Etchebest, et al.. Multiple interests in structural models of DARC transmembrane protein.. Transfusion Clinique et Biologique, Elsevier, 2010, 17 (3), pp.184-96. ⟨10.1016/j.tracli.2010.05.003⟩. ⟨inserm-00506537⟩
  • Olivia Doppelt-Azeroual, François Delfaud, Fabrice Moriaud, Alexandre de Brevern. Fast and automated functional classification with MED-SuMo: an application on purine-binding proteins.: functional classification with MED-SuMo §. Protein Science, Wiley, 2010, 19 (4), pp.847-67. ⟨10.1002/pro.364⟩. ⟨inserm-00458093⟩
  • Alexandre de Brevern. 3D Structural Models of Transmembrane Proteins.. Methods in Molecular Biology, Humana Press/Springer Imprint, 2010, 654, pp.387-401. ⟨10.1007/978-1-60761-762-4_20⟩. ⟨inserm-00507094⟩
  • Vincent Jallu, Mathilde Dusseaux, Simon Panzer, Marie-Françoise Torchet, Nathalie Hezard, et al.. AlphaIIbbeta3 integrin: new allelic variants in Glanzmann thrombasthenia, effects on ITGA2B and ITGB3 mRNA splicing, expression, and structure-function.: New mutations in Glanzmann patients and carriers. Human Mutation, Wiley, 2010, 31 (3), pp.237-46. ⟨10.1002/humu.21179⟩. ⟨inserm-00448024⟩
  • Alexandre de Brevern. Observer avec un nouvel oeil la structure des protéines et leur flexibilité.. Regard sur la biochimie, Société de chimie biologique, 2010, 2010 (4), pp.3. ⟨inserm-00557286⟩
  • Jean Pylouster, Aurélie Bornot, Catherine Etchebest, Alexandre de Brevern. Influence of assignment on the prediction of transmembrane helices in protein structures.. Amino Acids, Springer Verlag, 2010, 39 (5), pp.1241-54. ⟨10.1007/s00726-010-0559-6⟩. ⟨inserm-00472869⟩
  • Amine Ghozlane, Agnel Joseph, Aurélie Bornot, Alexandre de Brevern. Analysis of protein chameleon sequence characteristics.. Bioinformation, Biomedical Informatics Publishing Group, 2009, 3 (9), pp.367-9. ⟨inserm-00353122⟩
  • Cristina Benros, Alexandre de Brevern, Serge A. Hazout. Analyzing the sequence-structure relationship of a library of local structural prototypes.: Sequence-Structure Relationship. Journal of Theoretical Biology, Elsevier, 2009, 256 (2), pp.215-26. ⟨10.1016/j.jtbi.2008.08.032⟩. ⟨inserm-00318954⟩
  • Ksenia Oguievetskaia, Laetitia Martin-Chanas, Artem Vorotyntsev, Olivia Doppelt-Azeroual, Xavier Brotel, et al.. Computational fragment-based drug design to explore the hydrophobic sub-pocket of the mitotic kinesin Eg5 allosteric binding site.. Journal of Computer-Aided Molecular Design, Springer Verlag, 2009, 23 (8), pp.571-82. ⟨10.1007/s10822-009-9286-z⟩. ⟨inserm-00396557⟩
  • Manoj Tyagi, Aurélie Bornot, Bernard Offmann, Alexandre de Brevern. Analysis of loop boundaries using different local structure assignment methods.: loop boundary behaviors. Protein Science, Wiley, 2009, 18 (9), pp.1869-81. ⟨10.1002/pro.198⟩. ⟨inserm-00392504⟩
  • Alexandre de Brevern. Editorial for Infectious Diseases - Drug Targets (in silico issue). Infectious disorders drug targets, 2009, 9 (3), pp.246-7. ⟨inserm-00395256⟩
  • Aurélie Bornot, Catherine Etchebest, Alexandre de Brevern. A new prediction strategy for long local protein structures using an original description.. Proteins - Structure, Function and Bioinformatics, Wiley, 2009, 76 (3), pp.570-87. ⟨10.1002/prot.22370⟩. ⟨inserm-00348740⟩
  • Manoj Tyagi, Aurélie Bornot, Bernard Offmann, Alexandre de Brevern. Protein short loop prediction in terms of a structural alphabet.: protein short loops prediction. Computational Biology and Chemistry, Elsevier, 2009, 33 (4), pp.329-33. ⟨10.1016/j.compbiolchem.2009.06.002⟩. ⟨inserm-00396485⟩
  • Guilhem Faure, Aurélie Bornot, Alexandre de Brevern. Analysis of protein contacts into Protein Units.. Biochimie, Elsevier, 2009, 91 (7), pp.876-87. ⟨10.1016/j.biochi.2009.04.008⟩. ⟨inserm-00375095⟩
  • Olivia Doppelt-Azeroual, Fabrice Moriaud, François Delfaud, Alexandre de Brevern. Analysis of HSP90-related folds with MED-SuMo classification approach.. Drug Design, Development and Therapy, Dove Medical Press, 2009, 3, pp.59-72. ⟨inserm-00348737⟩
  • Alexandre de Brevern, Ludovic Autin, Yves Colin, Olivier Bertrand, Catherine Etchebest. In Silico Studies on DARC.. Infectious disorders drug targets, 2009, 9 (3), pp.289-303. ⟨inserm-00366309⟩
  • Juliette Martin, Alexandre de Brevern, Anne-Claude Camproux. In silico local structure approach: A case study on Outer Membrane Proteins.. Proteins - Structure, Function and Bioinformatics, Wiley, 2008, 71 (1), pp.92-109. ⟨10.1002/prot.21659⟩. ⟨inserm-00176452⟩
  • Guilhem Faure, Aurélie Bornot, Alexandre de Brevern. Protein contacts, inter-residue interactions and side-chain modelling.: protein contacts. Biochimie, Elsevier, 2008, 90 (4), pp.626-39. ⟨10.1016/j.biochi.2007.11.007⟩. ⟨inserm-00189828⟩
  • Bernard Offmann, Manoj Tyagi, Alexandre de Brevern. Local Protein Structures. Current Bioinformatics, Benthams Science, 2007, 2, pp.165-202. ⟨inserm-00175058⟩
  • Aurélie Bornot, Bernard Offmann, Alexandre de Brevern. How flexible protein structures are? New questions on the protein structure plasticity.. BioForum Europe, 2007, pp.24. ⟨inserm-00189079⟩
  • Olivia Doppelt, Fabrice Moriaud, Aurélie Bornot, Alexandre de Brevern. Functional annotation strategy for protein structures: Functional annotation strategy for protein structures. Bioinformation, Biomedical Informatics Publishing Group, 2007, 1 (9), pp.357-359. ⟨inserm-00143366⟩
  • Catherine Etchebest, Cristina Benros, Aurélie Bornot, Anne-Claude Camproux, Alexandre de Brevern. A reduced amino acid alphabet for understanding and designing protein adaptation to mutation.. European Biophysics Journal, Springer Verlag (Germany), 2007, 36 (8), pp.1059-69. ⟨10.1007/s00249-007-0188-5⟩. ⟨inserm-00155390⟩
  • Manoj Tyagi, Alexandre de Brevern, Narayanaswamy Srinivasan, Bernard Offmann. Protein structure mining using a structural alphabet.: Protein structure mining using a structural alphabet. Proteins - Structure, Function and Bioinformatics, Wiley, 2007, 71 (2), pp.920-937. ⟨10.1002/prot.21776⟩. ⟨inserm-00176443⟩
  • Alexandre de Brevern, Catherine Etchebest, Cristina Benros, Serge A. Hazout. "Pinning strategy": a novel approach for predicting the backbone structure in terms of protein blocks from sequence.. Journal of Biosciences, Indian Academy of Sciences, 2007, 32 (1), pp.51-70. ⟨inserm-00143368⟩
  • Jean-Christophe Gelly, Alexandre de Brevern, Serge A. Hazout. 'Protein Peeling': an approach for splitting a 3D protein structure into compact fragments.. Bioinformatics, Oxford University Press (OUP), 2006, 22 (2), pp.129-33. ⟨10.1093/bioinformatics/bti773⟩. ⟨inserm-00133725⟩
  • Cristina Benros, Alexandre de Brevern, Catherine Etchebest, Serge A. Hazout. Assessing a novel approach for predicting local 3D protein structures from sequence.. Proteins - Structure, Function and Bioinformatics, Wiley, 2006, 62 (4), pp.865-80. ⟨10.1002/prot.20815⟩. ⟨inserm-00133180⟩
  • Manoj Tyagi, Venkataraman S. Gowri, Narayanaswamy Srinivasan, Alexandre de Brevern, Bernard Offmann. A substitution matrix for structural alphabet based on structural alignment of homologous proteins and its applications.. Proteins - Structure, Function and Bioinformatics, Wiley, 2006, 65 (1), pp.32-9. ⟨10.1002/prot.21087⟩. ⟨inserm-00133760⟩
  • Manoj Tyagi, Priyanka Sharma, C. S. Swamy, Frédéric Cadet, N. Srinivasan, et al.. Protein Block Expert (PBE): a web-based protein structure analysis server using a structural alphabet.. Nucleic Acids Research, Oxford University Press, 2006, 34 (Web Server issue), pp.W119-23. ⟨10.1093/nar/gkl199⟩. ⟨inserm-00133751⟩
  • Jean-Christophe Gelly, Catherine Etchebest, Serge A. Hazout, Alexandre de Brevern. Protein Peeling 2: a web server to convert protein structures into series of protein units.. Nucleic Acids Research, Oxford University Press, 2006, 34 (Web Server issue), pp.W75-8. ⟨10.1093/nar/gkl292⟩. ⟨inserm-00133731⟩
  • Aurélie Bornot, Alexandre de Brevern. Protein beta-turn assignments.: Protein beta-turn assignments. Bioinformation, Biomedical Informatics Publishing Group, 2006, 1 (5), pp.153-5. ⟨inserm-00133658⟩
  • Catherine Etchebest, Cristina Benros, Serge A. Hazout, Alexandre de Brevern. A structural alphabet for local protein structures: improved prediction methods.. Proteins - Structure, Function and Bioinformatics, Wiley, 2005, 59 (4), pp.810-27. ⟨10.1002/prot.20458⟩. ⟨inserm-00143564⟩
  • Alexandre de Brevern, H. Wong, Christophe Tournamille, Yves Colin, Caroline Le van Kim, et al.. A structural model of a seven-transmembrane helix receptor: the Duffy antigen/receptor for chemokine (DARC).. BBA - Biochimica et Biophysica Acta, Elsevier, 2005, 1724 (3), pp.288-306. ⟨10.1016/j.bbagen.2005.05.016⟩. ⟨inserm-00143373⟩
  • Alexandre de Brevern. New assessment of a structural alphabet.. In Silico Biol, 2005, 5 (3), pp.283-9. ⟨inserm-00132875⟩
  • Juliette Martin, Guillaume Letellier, Antoine Marin, Jean-François Taly, Alexandre de Brevern, et al.. Protein secondary structure assignment revisited: a detailed analysis of different assignment methods.. BMC Structural Biology, BioMed Central, 2005, 5 (17), pp.17. ⟨10.1186/1472-6807-5-17⟩. ⟨inserm-00090199⟩
  • Laurent Fourrier, Cristina Benros, Alexandre de Brevern. Use of a structural alphabet for analysis of short loops connecting repetitive structures.. BMC Bioinformatics, BioMed Central, 2004, 5, pp.58. ⟨10.1186/1471-2105-5-58⟩. ⟨inserm-00112104⟩
  • Alexandre de Brevern, Cristina Benros, Romain Gautier, Hélène Valadié, Serge A. Hazout, et al.. Local backbone structure prediction of proteins.. In Silico Biol, 2004, 4 (3), pp.381-6. ⟨inserm-00132872⟩
  • Alexandre de Brevern, Serge A. Hazout, Alain Malpertuy. Influence of microarrays experiments missing values on the stability of gene groups by hierarchical clustering.. BMC Bioinformatics, BioMed Central, 2004, 5, pp.114. ⟨10.1186/1471-2105-5-114⟩. ⟨inserm-00000113⟩
  • Alexandre de Brevern, Serge A. Hazout. 'Hybrid protein model' for optimally defining 3D protein structure fragments.. Bioinformatics, Oxford University Press (OUP), 2003, 19 (3), pp.345-53. ⟨10.1093/bioinformatics/btf859⟩. ⟨inserm-00133632⟩
  • Alexandre de Brevern, France Loirat, Anne Badel-Chagnon, Cécile André, Pierre Vincens, et al.. Genome compartimentation by a hybrid chromosome model (HXM). Application to Saccharomyces cerevisae subtelomeres. Comput Chem, 2002, 26 (5), pp.437-45. ⟨10.1016/S0097-8485(02)00006-2⟩. ⟨inserm-00143383⟩
  • Alexandre de Brevern. Compartimentation chromosomique: Compartimentation chromosomique. Biofutur, Elsevier - Cachan : Lavoisier, 2002, 225, pp.20-22. ⟨inserm-00132826⟩
  • Alexandre de Brevern, Hélène Valadié, Serge A. Hazout, Catherine Etchebest. Extension of a local backbone description using a structural alphabet: a new approach to the sequence-structure relationship.. Protein Science, Wiley, 2002, 11 (12), pp.2871-86. ⟨inserm-00143374⟩
  • Alexandre de Brevern, Serge A. Hazout. Compacting local protein folds with a Hybrid Protein: Compacting local protein folds. Theoretical Chemistry Accounts: Theory, Computation, and Modeling, Springer Verlag, 2001, 106 (1/2), pp.36-47. ⟨10.1007/s002140000227⟩. ⟨inserm-00132867⟩
  • Anne-Claude Camproux, Alexandre de Brevern, Serge A. Hazout, Pierre Tufféry. Exploring the use of a structural alphabet for a structural prediction of protein loops. Theoretical Chemistry Accounts: Theory, Computation, and Modeling, Springer Verlag, 2001, 106 (1/2), pp.28-35. ⟨10.1007/s002140100261⟩. ⟨inserm-00134555⟩
  • Alexandre de Brevern, Catherine Etchebest, Serge A. Hazout. Bayesian probabilistic approach for predicting backbone structures in terms of protein blocks.. Proteins - Structure, Function and Bioinformatics, Wiley, 2000, 41 (3), pp.271-87. ⟨inserm-00132821⟩

Conference papers8 documents

  • Alexandre de Brevern. Analysis of allosteric effect of pathologic variants at the light of local protein conformations. Belgrade BioInformatics Conference – BelBi 2018, Jun 2018, Belgrade, Serbia. ⟨inserm-01853665⟩
  • Alexandre de Brevern. Protein structure analysis, prediction and flexibility in the light of a structural alphabet. 1ère réunion du GT MASIM du GDR BIM, GDR BIM (CNRS), Nov 2017, Paris, France. ⟨inserm-01636581⟩
  • Nicolas Shinada, Tarun Jairaj Narwani, Pierrick Craveur, Hubert Santuz, Joseph Rebehmed, et al.. Dynamics and deformability of α-, 310- and π-helices. 20e congrès du GGMM (groupe de graphisme et modélisation moléculaire), May 2017, Reims, France. ⟨inserm-01581259⟩
  • Bernard Offmann, M. Tyagi, A. Joseph, M. Drula, M. Grondin, et al.. PB-PENTAdb : a web resource for the analysis and prediction of local backbone structure and flexibility using pentapeptide protein blocks. 9th European Congress on Computation Biology (ECCB10), Sep 2010, Ghent, Belgium. ⟨hal-01198468⟩
  • Cristina Benros, Alexandre de Brevern, Serge Hazout. Hybrid Protein Model (HPM) : A Method For Building A Library Of Overlapping Local Structural Prototypes. Sensitivity Study And Improvements Of The Training: New developments of the Hybrid Protein Model. 2003, pp.53-72. ⟨inserm-00133639⟩
  • Cristina Benros, Serge A. Hazout, Alexandre de Brevern. "Hybrid Protein Model": a new clustering approach for 3D local structures: Evolution of Hybrid Protein Model. 2002, pp.36-45. ⟨inserm-00134559⟩
  • Alexandre de Brevern, Serge A. Hazout. Hybrid Protein Model (HPM): a method to compact protein 3D-structures information and physicochemical properties.. 2000, pp.49-54, ⟨10.1109/SPIRE.2000.878179⟩. ⟨inserm-00132863⟩
  • Alexandre de Brevern, Serge A. Hazout. "Hybrid Protein Model (HPM)" : une nouvelle approche pour caractériser les relations séquence-structure dans les protéines. 2000, pp.105-112. ⟨inserm-00134567⟩

Poster communications2 documents

  • Alexandre de Brevern, Jérémy Esque. Comparative Analysis of Protein -Protein Interface Methods. Groupe Graphisme Modélisation Moléculaire (GGMM), May 2017, Reims, France. ⟨inserm-01586501⟩
  • Alexandre de Brevern. On the turning away. 20e congrès du GGMM (groupe de graphisme et modélisation moléculaire), Aug 2017, Reims, France. 2017. ⟨inserm-01575727⟩

Books1 document

  • Gilbert Deléage, Manolo Gouy, Alexandre de Brevern. Bioinformatique - 3e édition : De la séquence à la structure des protéines. Dunod, 2021, Collection Sciences Sup, 978-2-10-081515-9. ⟨hal-03356596⟩

Book sections9 documents

  • Jean-Christophe Gelly, Alexandre de Brevern. A bioinformatic web server to cut protein structures in terms of Protein Units.. Jaclyn E. Morris. Computer Science Research and the Internet, Nova Book Press, pp.169-183, 2011. ⟨inserm-00646177⟩
  • Olivier Gascuel, P. Benas, C. Brun, D. Burnouf, Alexandre de Brevern, et al.. Modélisation des systèmes biologiques, bioinformatique. Rapport de conjoncture 2010 du Comité national de la recherche scientifique, CNRS Editions, chapitre 43, 845-858, 2011, ISBN 978-2-271-07263-4. ⟨hal-00799641⟩
  • Garima Agarwal, Dhurvas Chandrasekaran Dinesh, Narayanaswamy Srinivasan, Alexandre de Brevern. Characterization of Conformational Patterns in Active and Inactive Forms of Kinases Using Protein Blocks Approach.. 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⟩. ⟨inserm-00557296⟩
  • Agnel Joseph, Aurélie Bornot, Alexandre de Brevern. Local Structure Alphabets. Huzefa Rangwala, George Karypis. Introduction to Protein Structure Prediction: Methods and Algorithms, Wiley, pp.75-106, 2010, ⟨10.1002/9780470882207.ch5⟩. ⟨inserm-00557300⟩
  • Cristina Benros, Juliette Martin, Manoj Tyagi, Alexandre de Brevern. Description of the local protein structure. I. Classical approaches.. Alexandre G. de Brevern. Recent Advances in Structural Bioinformatics, Research Signpost, Trivandrum, Kerala, India., pp.6-27, 2007. ⟨inserm-00176471⟩
  • Manoj Tyagi, Cristina Benros, Juliette Martin, Alexandre de Brevern. Description of the local protein structure. II. Novel approaches.: structural alphabet. Alexandre G. de Brevern. Recent Advances in Structural Bioinformatics, Research Signpost, Trivandrum, Kerala, India., pp.28-42, 2007. ⟨inserm-00176668⟩
  • Patrick Fuchs, Catherine Etchebest, Alexandre de Brevern. Turns prediction: Turns prediction. Alexandre G. de Brevern. Recent Advances in Structural Bioinformatics, Research Signpost, Trivandrum, Kerala, India., pp.43-63, 2007. ⟨inserm-00176710⟩
  • Alexandre de Brevern, Cristina Benros, Serge A. Hazout. Structural Alphabet: From a Local Point of View to a Global Description of Protein 3D Structures. Yan, Peter V. Bioinformatics: New Research, Nova publishers, pp.127-69, 2005. ⟨inserm-00134564⟩
  • Alexandre de Brevern, Anne-Claude Camproux, Serge A. Hazout, Catherine Etchebest, Pierre Tufféry. Protein structural alphabets: beyond the secondary structure description: Structural alphabet : A review. Sangadai SG. Recent research developments in protein engineering, Research signpost, pp.319-331, 2001. ⟨inserm-00133650⟩

Preprints, Working Papers, ...1 document

  • Vincent Demolombe, Alexandre de Brevern, Liza Felicori, Christophe Nguyen, Ricardo Andrez Machado de Avila, et al.. PEPOP: new approaches to mimic non-continous epitopes. 2018. ⟨hal-02787634⟩

Theses1 document

  • Alexandre de Brevern. Nouvelles stratégies d'analyses et de prédiction des structures tridimensionnelles des protéines. Biochimie [q-bio.BM]. Université Paris-Diderot - Paris VII, 2001. Français. ⟨tel-00133819⟩