Alexandre G. de Brevern's publications

2022 - 2021 - 2020 - 2019 - 2018 - 2017 - 2016 - 2015 - 2014 - 2013 - 2012 - 2011 - 2010 - 2009 - 2008 - 2007 - 2006 - 2005 - 2004 - 2003 - 2002 - 2001 - 2000 ( Related works)
pubmed HAL INSERM

Year 2023

  1. Tourlet S., Radjasandirane R., Diharce C., de Brevern A.G.*.
    AlphaFold2 Update and Perspectives
    BioMedInformatics (2023) 3(2), 378-390.

  2. Teletechea S., Esque J., Urbain A., Etchebest C., de Brevern A.G.*.
    Evaluation of Transmembrane Protein Structural Models Using HPMScore
    BioMedInformatics (2023) 3(2), 306-326.

  3. < Radjasandirane R., de Brevern A.G.*.
    Structural and Dynamic Differences between Calreticulin Mutants Associated with Essential Thrombocythemia
    Biomolecules (2023) 13(3):509

  4. Vattekatte A.M.*, Diharce, J., Rebehmed J., Cadet, F., Gardebien, F., Etchebest, C., de Brevern A.G.*.
    General Trends of the Camelidae Antibody VHHs Domain Dynamics
    Int J mol Sci (2023) 24(5):4511

  5. Foga J., de Brevern A.G.#, Diharce J.#
    Conformational and Binding Mode Assessment of the Human IL-3 Recognition By Its Alpha Receptor.
    Proteins (2023) in press.

  6. Nadaradjane A.A.#, Diharce J., Rebehmed J., Cadet F., Gardebien F., Gelly J.-C., Etchebest C., de Brevern A.G.#
    Quality assessment of vhh models.
    J Biol Struct Dyn (2023) 8:1-15.

  7. Floch A.#, Lomas-Francis C., Vege S., Brennan S., Shakarian G., de Brevern A.G., Westhoff C.M.
    A novel high prevalence antigen in the lutheran system, luga (lu24), and an updated, full-length 3d bcam model.
    Transfusion (2023) 63(4):798-807.

  8. de Brevern A.G.#
    An agnostic analysis of the human AlphaFold2 proteome using local protein conformations.
    Biochimie (2023) 207:11-19.

  9. Floch A.#, Lomas-Francis C., Vege S., Burgos A., Hoffman R., Cusik R. de Brevern A.G., Westhoff C.M.
    Two new Scianna variants causing loss of high prevalence antigens: ERMAP model and 3D analysis of the antigens.
    Transfusion (2023) 63(1):230-238.

Year 2022

  1. de Brevern A.G.#
    A perspective on the (rise and fall of) protein β-turns.
    Int J mol Sci (2022) 23(20):12314.

  2. Cretin G., Galochkina T., Vander Meersche Y., de Brevern A.G., Postic G., Gelly J.-C.#
    SWORD2: hierarchical analysis of protein 3D structures.
    Nucleic Acid Res (2022) 50(W1):W732-8.

  3. Vishwakarma P.+, Vattekatte A.M.+, Shinada, N.o, Diharce, J.o, Martins, C., Cadet, F., Gardebien, F., Etchebest, C., Nadaradjane, A.A.*, de Brevern A.G.*,#.
    VHH Structural Modelling Approaches: A Critical Review.
    Int J mol Sci (2022) 23(7):3721

  4. Maljković M.M.#, Mitić N.S., de Brevern A.G.
    Prediction of Structural Alphabet Protein Blocks Using Data Mining.
    Biochimie (2022) 197:74-85

  5. Rebehmed J.#, de Brevern A.G.#, Sowdhamini R.#, Joseph A.P.#
    Editorial: Advances in Molecular Docking and Structure-Based Modelling.
    Front Mol Sci (2022) 9:839826.

  6. Sali A., Jallu V., Diharce J., Narwani T.J.#, de Brevern A.G.#
    Analysis of Integrin alphaIIb subunit dynamics reveals long-range effects of missense mutations on Calf domains.
    Int J mol Sci (2022) 23(2):858.

  7. de Brevern A.G.#, Rebehmed J.#
    Current status of PTMs structural databases: applications, limitations and prospects.
    Amino Acids (2022) 54(4):575-590.

  8. El Jahrani N., Cretin C., de Brevern A.G.#
    CALR-ETdb, the database of calreticulin variants diversity in essential thrombocythemia.
    Platelets (2022) 33(1):157-167.

  9. Koker M.Y., Sarper N., Albayrak C., Zulfikar B., ZenginE, Saraymen B., Albayrak D., Koc B., Avcilar H., Karakukcu M., Chenet C., Bianchi F., de Brevern A.G., Petermann R., Jallu V.#
    New alphaIIbbeta3 variants in 28 Turkish Glanzmann patients; Structural hypothesis for complex activation by residues variations in I-EGF domains
    Platelets (2022) 33(4):551-561.

  10. Craveur P., Narwani T.J., Srinivasan N., Gelly J.-C., Rebehmed J.#, de Brevern A.G.#
    Shaking the beta-bulges
    IEEE/ACM Transactions on Computational Biology and Bioinformatics (2022) 19(1):14-18

  11. Rebehmed J., de Brevern A.G., Sowdhamini R., Joseph A.P.
    Research Topic Advances in Molecular Docking and Structure-Based Modelling [e-book : pdf ]
    Frontiers in Molecular Biosciences (2022).

  12. de Brevern A.G.
    Recent Developments on Protein–Ligand Interactions: From Structure, Function to Applications [e-book : pdf ]
    Int J mol Sci - MDPI (2022).

Year 2021

  1. Cretin G., Galochkina T., de Brevern A.G.,Gelly J.-C.#
    PYTHIA: Deep Learning Approach For Local Protein Conformation Prediction
    Int J Mol Sci (2021) 22(16):8831.

  2. Nekrasov A.N., Kozmin Y.P., Kozyrev S.V., Ziganshin R.H., de Brevern A.G., Anashkina A.A.#
    Hierarchical structure of protein sequence
    Int J Mol Sci (2021) 22(15):8339.

  3. Fogha J. Bayry J., Diharce J.#, de Brevern A.G.#
    Structural and evolutionary exploration of the IL-3 family and its alpha subunit receptors
    Amino Acids (2021) 53(8):1211-1227.

  4. Floch A., Teletchea S., Tournamille C., de Brevern A.G., Pirenne F.#
    A Review of the Literature Organized Into a New Database: RHeference
    J Transfus Med Rev. (2021) 35(2):70-77.

  5. Buks R., Brusson M., Cochet S., Galochkina T., Cassinat B., Nemazanyy I., Peyrard T., Kiladjian J.J., de Brevern A.G., Azouzi S., El Nemer W.#
    ABCG2 Is Overexpressed on Red Blood Cells in Ph-Negative Myeloproliferative Neoplasms and Potentiates Ruxolitinib-Induced Apoptosis
    Int J Mol Sci (2021) 22(7):3530.

  6. Ravikumar A., de Brevern A.G., Srinivasan N.#
    Conformational Strain Indicated by Ramachandran Angles for the Protein Backbone is Only Weakly Related to the Flexibility
    J Phys Chem (2021) 125(10):2597-2606.

  7. Deleage G., Gouy M., de Brevern A.G.
    Bioinformatique - 3e ed - de la sequence a la structure des proteines. (book in french)
    DUNOD (2021) 227 pages.

  8. Vander Meersche Y. Cretin G., de Brevern A.G., Gelly J.-C.#, Galochkina T.#
    MEDUSA: Prediction of protein flexibility from sequence.
    J Mol Biol (2021) 433(11):166882.

  9. Floch A.#, Pirenne F., Barrault A., Chami B., Toly-Ndour C., Tournamille C., de Brevern A.G.#
    Insights into anti-D formation in carriers of RhD variants through studies of 3D intraprotein interactions.
    Transfusion (2021) 61(4):1286-1301.

  10. Melarkode Vattekatte A., Cadet F.,Gelly J.-C., de Brevern A.G.#
    Insights into comparative modeling of VHH domains
    Int J Mol Sci (2021) 22(18):9771.

  11. Tandon H., de Brevern A.G., Srinivasan N.#
    Transient association between proteins elicits alteration of dynamics at sites far away from interfaces.
    Structure (2021) 29(4):371-384.

Year 2020

  1. de Brevern A.G.#
    Impact of protein dynamics on secondary structure prediction.
    Biochimie (2020) 179:14-22.

  2. Hill A., Karboune S.#, Narwani T.J., de Brevern A.G.
    Investigating the product profiles and structural relationships of new levansucrases with conventional and non-conventional substrates.
    Int J Mol Sci (2020) 21(15):E5402.

  3. de Brevern A.G.#
    Analysis of Protein Disorder Predictions in the light of Protein Structural Alphabet.
    Biomolecules (2020) 10(7):E1080.

  4. Shinada N.K., Schmidtke P., de Brevern A.G.#
    Accurate Representation of Protein-Ligand Structural Diversity in the Protein Data Bank (PDB).
    Int J Mol Sci (2020) 21(6):2243.

  5. Melarkode Vattekatte A., Narwani T.J., Floch A., Maljkovic M., Bisoo S., Shinada N.K., Kranjc A., Gelly J.-C., Srinivasan N., Mitic N., de Brevern A.G.#
    Data set of Intrinsically Disordered Proteins analysed at a local protein conformation level.
    Data in Brief (2020) 29:105383.

  6. Melarkode Vattekatte A., Shinada N.K., Narwani T.J., Noel F., Bertrand O. Meyneil J.-P., Malpertuy A., Gelly J.-C., Cadet F., de Brevern A.G.#
    Discrete analysis of camelid variable domains: sequences, structures, and in- silico structure prediction.
    Peer J. (2020) 8:e8408.

  7. Melarkode Vattekatte A., Narwani T.J., Floch A., Maljkovic M., Bisoo S., Shinada N.K., Kranjc A., Gelly J.-C., Srinivasan N., Mitic N., de Brevern A.G.#
    A structural entropy index to analyse local conformations in intrinsically disordered proteins.
    J Struct Biol. (2020) 2020:107464.

  8. Narwani T.J.*, Craveur P.*, Shinada N.K.*, Floch A., Santuz H., Melarkode Vattekatte A., Srinivasan N., Rebehmed J., Gelly J.-C., Etchebest C., de Brevern A.G.#
    Discrete analyses of protein dynamics
    JBSD (2020) 12:1-15.

Year 2019

  1. Faure G., Joseph A.P., Craveur P., Narwani T.J., Srinivasan N., Gelly J.-C.,Rebehmed J.*, de Brevern A.G.#*
    iPBAvizu: a PyMOL plugin for an efficient 3D protein structure superimposition approach.
    Source Code for Biology and Medicine (2019) 14:5.

  2. Vetrivel I., de Brevern A.G., Cadet F., Srinivasan N., Offmann B#
    Structural variations within proteins can be as large as variations observed across their homologues.
    Biochimie (2019) 167:162-70.

  3. Narwani T.J., Etchebest C..*, Craveur P., Leonard S., Rebehmed J., Srinivasan N., Bornot A., Gelly J.-C., de Brevern A.G.#
    in silico prediction of protein flexibility with local structure approach.
    Biochimie (2019) 165:150-155.

  4. Demolombe V, de Brevern A.G., Molina F, Lavigne G, Granier C, Moreau V. #
    Benchmarking the PEPOP methods for mimicking discontinuous epitopes.
    BMC Bioinformatics (2019) 20(1):738.

  5. Guadall A., Cochet S., Renaud O., Colin Y., Le Van Kim C.,de Brevern A.G., El Nemer W.#
    Dimerization and phosphorylation of Lutheran/basal cell adhesion molecule are critical for its function in cell migration on laminin
    J Biol Chem (2019) 294(41):14911-21.

  6. Craveur P.*, Narwani T.*, Rebehmed J.#, de Brevern A.G.#
    Investigate the impact of PTMs on the protein backbone conformation.
    Amino Acids (2019) 51(7):1065-1079.

  7. Shinada N.K.#, de Brevern A.G., Schmidtke P.
    Halogens in Protein-Ligand Binding Mechanism: A Structural Perspective.
    J Med Chem (2019) 62(21):9341-9356.

  8. Demolombe V, de Brevern A.G., Felicori L, NGuyen C, Machado de Avila RA, Valera L, Jardin-Watelet B, Lavigne G, Lebreton A, Molina F, Moreau V#
    PEPOP 2.0: new approaches to mimic non-continuous epitopes.
    BMC Bioinformatics (2019) 20(1):387.

  9. Nekrasov AN, Alekseeva LG, Pogosyan RA, Dolgikh DA, Kirpichnikov MP, de Brevern A.G.#, Anashkina AA
    A minimum set of stable blocks for rational design of polypeptide chains.
    Biochimie (2019) 160:88-92.

  10. Wajcman H. de Brevern A.G., Riou J., Latouche C., Marden M.C., Pissard S.#
    Short in-Frame Insertions/Deletions in the Coding Sequence of the alpha-Globin Gene. Consequences of the 3D Structure and Resulting Phenotypes: Hb Choisy as an Example.
    Hemoglobin (2019) 42:287-293.

  11. Kalaivani R., Narwani T.J., de Brevern A.G., Srinivasan N.#
    Long-range molecular dynamics show that inactive forms of Protein Kinase A are more dynamic than active forms.
    Protein Science (2019) 28:543-560.

  12. Ruppë E.#, Ghozlane A., Tap J., Pons N., Alvarez A.-S., Maziers N., Cuesta T., Hernando-Amado S., Clares I., Martinez J.L., Coque T.M., Baquero F., Lanza V.F., Maiz L., Goulenok T., de Lastours V., Amor N., Fantin B., Ingrid Wieder I., Andremont A., van Schaik W., Rogers M., Zhang X., Willems R.J.L., de Brevern A.G., Batto J.-M., Blottiëre H., Lëonard P., Lëjard V., Letur A., Levenez F., Weiszer K., Haimet F., Dorë J., Kennedy S.P., Dusko Ehrlich S.
    Prediction of the intestinal resistome by a novel 3D-based method.
    Nat Microbiol (2019) 4(1):112-123.

Year 2018

  1. de Brevern A.G., Floch A., Barrault A., Martret J., Martret J., Bodivit G., Pirenne F., Tournamille C.#
    Alloimmunization risk associated with amino acid 223 substitution in the RhD protein: analysis in the light of molecular modeling.
    Transfusion (2018) 58(11):2683-2692.

  2. de Brevern A.G.#
    Analysing the Structural Effect of Point Mutations of Cytotoxic Necrotizing Factor 1 (CNF1) on Lu/BCAM Adhesion Glycoprotein Association.
    Toxins (Basel) (2018) 13;10(3). pii: E122.

  3. Vishwanath S., de Brevern A.G., Srinivasan N.#
    Same but not alike: Structure, flexibility and energetics of domains in multi-domain proteins are influenced by the presence of other domains.
    PLoS Comput Biol. (2018) 14(2):e1006008.

  4. Narwani T.J.*, Craveur P.*, Shinada N.K.*, Santuz H., Rebehmed J., Etchebest C., de Brevern A.G.#
    Dynamics and Deformability of α-, 310- and π-Helices.
    Archives of Biological Sciences (2018) 70(1):21-31.

Year 2017

  1. Vetrivel I., Mahajan S., Tyagi M., Hoffmann L., Sanejouand Y.H., Srinivasan N., de Brevern A.G., Cadet F., Offmann B#
    Knowledge-based prediction of protein backbone conformation using a structural alphabet.
    PLoS ONE (2017) 12(11):e0186215.

  2. Goguet M.*, Narwani T.J.*, Petermann R., Jallu V.+, de Brevern A.G.+#
    In silico analysis of Glanzmann variants of Calf-1 domain of αIIbβ3 integrin revealed dynamic allosteric.
    Sci Rep (2017) 7(1):8001.

  3. Bisagni S., Abolhalaj M., de Brevern A.G., Rebehmed J., Hatti-Kaul R.#, Mamo G.
    Enhancing the Activity of a Dietzia sp. D5 Baeyer-Villiger Monooxygenase towards Cyclohexanone by Saturation Mutagenesis.
    ChemistrySelect (2017) 2(24):7169–7177.

  4. Barnoud J., Santuz H., Craveur P., Joseph A.P., Jallu V., Poulain P.+#,de Brevern A.G.+#
    PBxplore: a tool to analyze local protein structure and deformability with Protein Blocks.
    PeerJ (2017) 5:e4013s.

  5. Narwani T.J., Santuz H., Shinada N.K., Melarkode Vattekatte A., Ghouzam Y., Srinivasan N., Gelly J.-C., de Brevern A.G.#
    Recent advances on polyproline II.
    Amino Acids (2017) 49(4):705-713.

  6. Floch A., Barrault A., de Brevern A.G., Martret J., Gaillard K., Devaux L., Chami B., Bierling P., Pirenne F., Tournamille C.#
    Molecular characterization of 13 new RHD alleles..
    Transfusion (2017) 57(4):1089-1091.

Year 2016

  1. Noël F., Malpertuy A., de Brevern A.G.#,
    Global analysis of VHHs framework regions with a structural alphabet.
    Biochimie (2016) 131:11-19.

  2. de Brevern A.G.#,
    Extension of the classical classification of β-turns.
    Sci Rep (2016) 6:33191.

  3. Ghouzam Y., Postic G., Guerin P.E., de Brevern A.G., Gelly J.-C.#
    ORION: a web server for protein fold recognition and structure prediction using evolutionary hybrid profiles.
    Sci Rep (2016) 6:28268.

  4. Kalaivani R., de Brevern A.G., Srinivasan N.#
    Conservation of structural fluctuations in homologous protein kinases and its implications on functional sites.
    Proteins (2017) 4(7):957-78..

Year 2015

  1. Ghouzam Y., Postic G., de Brevern A.G., Gelly J.-C.#
    Improving protein fold recognition with hybrid profiles combining sequence and structure evolution..
    Bioinformatics (2015) 31(23):3782-9.

  2. Seo S., Rebehmed J., de Brevern A.G., Karboune S.#
    Enzymatic Synthesis of Galactosylated Serine/Threonine Derivatives by ß-Galactosidase from Escherichia coli.
    Int. J. Mol. Sci. (2015) i16(6):13714-28.

  3. Esque J.,* Urbain A.*, Etchebest C.+, de Brevern A.G.+,#
    Sequence-Structure relationship study in all-alpha transmembrane proteins using an unsupervised learning approach.
    Amino Acids (2015) 47(11):2303-22.

  4. Craveur P., Joseph A.P., Esque J., Narwani T.J., Noël F., Shinada N., Goguet M., Leonard S., Poulain P., Bertrand O., Faure G., Rebehmed J., Ghozlane A., Swapna L.S., Bhaskara R.M., Barnoud J., Télétchéa S., Jallu V., Cerny J., Schneider B., Etchebest C., Srinivasan N., Gelly J.-C., de Brevern A.G.#
    Protein flexibility in the light of structural alphabets.
    Frontiers in Molecular Biosciences - Structural Biology (2015) 2:20.

  5. de Brevern A.G.#, Meyneil, J.-P., Fairhead C., Neuvéglise C., Malpertuy A.
    Trends in IT innovation to build a Next generation bioinformatics solution to manage and analyze biological big data produced by NGS technologies.
    BioMed Research International - Big Data Approaches for Biomedical Informatics (BIB) (2015) 2015:904541.

  6. Smolarek D., Hattab C., Buczkowska A., Kaczmarek R., Jarzab A., Cochet S., de Brevern A.G., Lukasiewicz J., Jachymek W., Niedziela T., Grodecka M., Wasniowska K., Colin-Aronovicz Y., Bertrand O., Czerwinski M. #
    Studies of a murine monoclonal antibody directed against DARC: reappraisal of its specificity.
    PLoS ONE (2015) 10(2):e0116472.

  7. Mahajan S., de Brevern A.G., Sanejouand Y.-H., Srinivasan N., Offmann B.#
    Use of a structural alphabet to find compatible folds for amino acid sequences
    Protein Science (2015) 24(1) 145–153.

    *,+: authors contribute equally. #: corresponding author(s).

Year 2014

  1. Chebrek R., Leonard S., de Brevern A.G., Gelly J.-C.#
    PolyprOnline : Polyproline helix II and secondary structure assignment database
    Database (2014) pii: bau102.

  2. Schneider B.#, Gelly J.-C., de Brevern A.G., Cerný J.
    Local dynamics of proteins and DNA evaluated from crystallographic B-factors
    Acta Crystallographica Section D (2014) 70(Pt 9):2413-9.

  3. Jallu V.*#, Poulain P.*, Fuchs P.F., Kaplan C., de Brevern A.G.#
    Modeling and molecular dynamics simulations of the V33 variant of the integrin subunit β3: structural comparison with the L33 (HPA-1a) and P33 (HPA-1b) variants
    Biochimie(2014) 105:84-90.

  4. Craveur P.*,#, Rebehmed J.*, de Brevern A.G.#
    PTM-SD: a database of structurally resolved and annotated post-translational modifications in proteins
    Database (2014) 2014: bau041.

  5. Joseph A.P.*,#, de Brevern A.G.*,#
    From local structure to a global framework: Recognition of protein folds
    Interface (2014) 11(95):20131147.

  6. Schneider B.#, Cerný J., Svozil D., Cech P., Gelly J.-C., de Brevern A.G.
    Bioinformatic analysis of the protein/DNA interface
    Nucl Acid Res (2014) 42(5):3381-94.

  7. Mahajan S., de Brevern A.G., , Offmann B., Srinivasan N.#
    Correlation between local structural dynamics of proteins inferred from NMR ensembles
    and evolutionary dynamics of homologues of known structure
    J Biol Struct Dyn (2014) 32(5):751-8.

  8. Leonard S.*, Joseph A.P.*, Srinivasan N., Gelly J.-C., de Brevern A.G.#
    mulPBA : an efficient multiple protein structure alignment method based on a structural alphabet
    J Biol Struct Dyn (2014) 32(4):661-8.

    *: authors contribute equally. #: corresponding author(s).

Year 2013

  1. Craveur P.#, Joseph A.P., Rebehmed J., de Brevern A.G.#
    β-bulges: Extensive structural analyses of ß-sheets irregularities
    Protein Science (2013) 22(10):1366-78.

  2. Mahajan, S., Iftekar M., Agarwal G., Offmann B., de Brevern A.G., N. Srinivasan#
    DoSA: Database of Structural Alignments
    Database (2013) 2013:48.

  3. Craveur P.*, Joseph A.P.*, Poulain P., Rebehmed J.+,#, de Brevern A.G.+,#
    Cis-trans isomerization of omega dihedrals in Proteins
    Amino Acids (2013) 45(2):279-89.

  4. Esque J.*, Léonard S.*, de Brevern A.G.+,#, Oguey C.+,#
    VLDP webserver: a powerful geometric tool for analysing protein structures in their environment
    Nucl Acid Res (2013) 41:W373–378.

  5. Chevrier L., de Brevern A.G., Hernandez E., Leprince J., Vaudry H., Guedj A.M., de Roux N.#
    PRR repeats in the intracellular domain of KISS1R are 1 important for its export to cell membrane
    Mol Endocr (2013) 27(6):1004-14.

  6. Rebhemed J, Alphand V, de Berardinis V, de Brevern A.G.#
    Evolution study of the Baeyer-Villiger monooxygenases enzyme family: functional importance of the highly conserved residues
    Biochimie (2013) 95(7):1394-402.

  7. Bhaskara R.M., de Brevern A.G., Srinivasan N.#
    Understanding the role of domain–domain linkers in the spatial orientation of domains in multi-domain proteins
    J Biol Struct Dyn (2013) 31(12):1467-80.

    *,+: authors contribute equally. #: corresponding author(s).

Year 2012

  1. Jallu V.*, Poulain P.*, Fuchs P.F., Kaplan C., de Brevern A.G.#
    Modeling and Molecular Dynamics of HPA-1a and -1b Polymorphisms: Effects on the Structure of the β3 Subunit of the αIIb/β3 Integrin
    Plos One(2012) 7(11):e47304.

  2. Gelly J.-C., Lin H.-Y., Chuang T.*, Chen F.-C.*, de Brevern A.G.*
    Selective Constraint on Human Pre-mRNA Splicing by Protein Structural Properties
    Genome Biology and Evolution (2012) 4(9):966-75.
    *: authors contribute equally.

  3. Joseph A.P., Srinivasan N., de Brevern A.G.
    Progressive structure-based alignment of homologous proteins: Adopting sequence comparison strategies
    Biochimie (2012) 94:2025-34.

  4. Joseph A.P., Valadie H., Srinivasan N., de Brevern A.G.
    Local structural differences in homologous proteins: Specificities in different SCOP classes
    Plos One (2012) 7(6): e38805.

  5. de Brevern A.G.*, Bornot A.*, Craveur P., Etchebest C., Gelly J.-C.
    PredyFlexy: Flexibility and Local Structure prediction from sequence
    Nucleic Acid Res (2012) 40:W317-22.
    *: authors contribute equally.

  6. Swapna L.S., Mahajan S., de Brevern A.G., Srinivasan N.
    Comparison of tertiary structures of proteins in protein-protein complexes with unbound forms suggests prevalence of allostery in signalling proteins.
    BMC Struct Biol (2012) 12:6.

  7. Joseph A.P., Srinivasan N., de Brevern A.G.
    Cis-trans peptide variations in structurally similar proteins
    Amino Acids (2012) 43(3):1369-81.

    *: authors contribute equally. #: corresponding author(s).

Year 2011

  1. Amiard A., Baczynski C., Blanchet C., de Brevern A.G., Dorlanne-Messiaen E., Grognard E., Kisselova G., Malpertuy A., Menez-Jamet J. , Racle I., Rouger C.
    Electronic laboratory notebook (eLN)
    STP Pharma Pratiques (2011), 21(6):475-503.

  2. J.-C. Gelly, Joseph A.P., Srinivasan N., de Brevern A.G.
    iPBA : A tool for protein structure comparison using sequence alignment strategies
    Nucleic Acid Res (2011) 39:W18-23.

  3. Joseph A.P., Srinivasan N., de Brevern A.G.
    Improvement of protein structure comparison using a structural alphabet
    Biochimie (2011) 93(9):1434-45.

  4. Mansiaux Y., Joseph A.P., Gelly J.-C., de Brevern A.G.
    Assignment of PolyProline II conformation and analysis of sequence - structure relationship
    PlosOne (2011) 6(3): e18401.

  5. Agarwal G., Mahajan S., Srinivasan N., de Brevern A.G.
    Identification of Local Conformational Similarity in Structurally Variable Regions of Homologous Proteins Using Protein Blocks
    PlosOne (2011) 6(3):e17826.

  6. Jallu V., Poulain P., Kaplan C., de Brevern A.G.
    3D protein structure modeling: A tool to provide insight into the platelet alloimmune response.
    Transfusion Today (2011) 86:10-11.

  7. de Brevern A.G., Joseph A.P.
    Species Specific Amino Acid Sequence - Protein Local Structure Relationships: an analysis in the light of a structural alphabet.
    J. Theo. Biol. (2011) 51(2):493-507.

  8. Esque J., Oguey C., de Brevern A.G.
    Comparative analysis of threshold and tessellation methods for determining protein contacts
    J. Chem. Inf. Model. (2011) 51(2):493-507.

  9. Bornot A., Etchebest C., de Brevern A.G.
    Predicting Protein Flexibility through the Prediction of Local Structures.
    Proteins (2011)79(3):839-52.

  10. Gelly J.-C., de Brevern A.G.
    Protein Peeling 3D: New tools for analyzing protein structures.
    Bioinformatics (2011) 27(1):132-3.

  11. Gelly J.-C., de Brevern A.G.
    A bioinformatic web server to cut protein structures in terms of Protein Units
    Computer Science Research and the Internet (2011)
    ISBN-13: 978-1617287305 - Jaclyn E. Morris. ed, Nova Book Press, 169-183.

  12. Rapport de conjoncture CoNRS section 16
    Chimie du Vivant et pour le Vivant : Conception et Propriétés de Molécules D’interêt Biologique.

  13. Rapport de conjoncture CNRS 43
    Modélisation des systèmes biologiques, bioinformatique.

Year 2010

  1. Arnaud L., Saison C., Helias V., Lucien N., Steschenko D., Giarratana M.-C., Claude Prehu C., Foliguet B., Montout L., de Brevern A.G., Francina A., Ripoche P., Fenneteau O., Da Costa L., Peyrard T., Coghlan G., Illum N., Birgens H., Tamary H., Iolascon A., Delaunay J., Tchernia G., Cartron J.-P.
    A dominant mutation in the gene encoding the erythroid transcription factor KLF1 causes a congenital dyserythropoietic anemia.
    The American Journal of Human Genetics (2010) 87(5):721-7.

  2. Joseph A.P., Agarwal G., Mahajan S., Gelly J.-C., Swapna L.S., Offmann B., Cadet F., Bornot A., Tyagi M., Valadié H., Schneider B., Etchebest C., Srinivasan N., de Brevern A.G.
    A short survey on Protein Blocks.
    Biophysical Reviews (2010) 2(3):137-145.

  3. Smolarek D., Bertrand O., Czerwinski M., Colin Y., Etchebest C., de Brevern A.G.
    Multiple interests in structural models of DARC transmembrane protein.
    Trans Clin Biol (2010) 17(3):184-196.

  4. Smolarek D., Hattab C., Hassanzadeh-Ghassabeh G., Cochet S., Gutiérrez C.,
    de Brevern A.G., Udomsangpetch R., Picot J., Grodecka M., Wasniowska K.,
    Muyldermans S., Colin Y., Le Van Kim C., Czerwinski M., Bertrand O.
    A recombinant dromedary antibody fragment (VHH or nanobody) directed against human Duffy Antigen Receptor for Chemokines
    Cellular and Molecular Life Sciences (2010) 67(19):3371-87.

  5. Esque J., Oguey C., de Brevern A.G.
    A Novel Evaluation of Residue and Protein Volumes by Means of Laguerre Tessellation
    J. Chem. Inf. Model. (2010) 50(5):947-60.

  6. Pylouster J., Bornot A., Etchebest C., de Brevern A.G.
    Influence of assignment on the prediction of transmembrane helices in protein structures
    Amino Acids (2010) 39(5):1241-54.

  7. de Brevern A.G.
    Observer avec un nouvel œil la structure des protéines et leur flexibilité.
    Regard Sur la Biochimie (2010) 4:3.

  8. Doppelt-Azeroual O., Delfaud F., Moriaud F., de Brevern A.G.
    Classification of binding sites with MED-SuMo Multi approach: an application on Purinome
    Protein Science (2010) 19(4):847-67.

  9. Celton M., Malpertuy A., Lelandais G., de Brevern A.G.
    Comparative analysis of missing value imputation methods to improve
    clustering and interpretation of microarray experiments
    BMC Genomics (2010) 11(1):15.

  10. Jallu V., Dusseaux M., Panzer S., Torchet M.F., Hezard N, Goudemand J., de Brevern A.G., Kaplan C.
    αIIb/β3 i integrin: new allelic variants in Glanzmann thrombasthenia, effects on ITGA2B and ITGB3 mRNA splicing, expression, and structure-function..
    Human Mutation (2010) 31(3):237-46.

  11. Agarwal G., Dinesh D.C., Srinivasan N., de Brevern A.G.
    Characterizatrion of conformational patterns in active and inactive forms of kinases using Protein Blocks approach
    Computational Intelligence and Pattern Analysis in Biological Informatics (2010)
    U. Maulik, S. Bandyopadhyay and J.T.L. Wang eds., Wiley, 169-188.

  12. Joseph A.P., Bornot A., de Brevern A.G.
    Local Structure Alphabets
    Protein Structure Prediction (2010)
    Huzefa Rangwala and George Karypis eds., Wiley, 75-106.

  13. de Brevern A.G.
    3D-structural models of transmembrane proteins
    Membrane protein structure determination: from structure to function
    Methods in Molecular Biology (2010) 654:387-401

Year 2009

  1. de Brevern A.G.
    New opportunities to fight against infectious diseases and to identify pertinent drug targets with novel methodologies
    Infectious Diseases - Drug Targets (2009) 9(3):246-7.

  2. Tyagi M., Bornot A., Offmann B., de Brevern A.G.
    Analysis of loop boundaries using different local structure assignment methods
    Protein Science (2009) 18(9):1869-81.

  3. Oguievetskaia K., Martin-Chanas L., Vorotyntsev A., Doppelt-Azeroual O., Brotel X., Adcock S.A., de Brevern A.G., Delfaud F., Moriaud F.
    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 (2009) 23 (8):571-82.

  4. Faure G., Bornot A., de Brevern A.G.
    Analysis of protein contacts into Protein Units
    Biochimie (2009) 91(7):876-87.

  5. Tyagi M., Bornot A., Offmann B., de Brevern A.G.
    Protein short loop prediction in terms of a structural alphabet
    Computational Biology and Chemistry (2009) 33:329-33

  6. de Brevern A.G., Autin L., Colin Y., Bertrand Y., Etchebest C.
    in silico studies on DARC
    Infectious Diseases - Drug Targets (2009) 9(3):289-303.

  7. Ghozlane A., Joseph A.P., Bornot A., de Brevern A.G.
    Analysis of protein chameleon sequence characteristics
    Bioinformation (2009) 3(9), 367-369.

  8. Bornot A., Etchebest C., de Brevern A.G.
    A new prediction strategy for long local protein structures using an original description
    Proteins (2009) 76(3):570-87.

  9. Doppelt-Azeroual O., Moriaud F., Delfaud F., de Brevern A.G.
    Analysis of HSP90 related folds with MED-SuMo classification approach
    Drug Design, Development and Therapy (2009) 3:59–72.

  10. Benros C., de Brevern A.G., Hazout S.
    Analyzing the sequence-structure relationship of a library of local structural prototypes
    J Theor Biol. (2009) 256(2):215-26.

Year 2008

  1. Faure G., Bornot A., de Brevern A.G.
    Protein contacts, inter-residue interactions and side-chain modelling
    Biochimie (2008) 90(4):626-39 - corrigendum 90(8):1264.

  2. Tyagi M., de Brevern A.G., Srinivasan N., Offmann B.
    Protein structure mining using a structural alphabet
    Proteins. (2008) 71(2):920-37

  3. Martin J., de Brevern A.G., Camproux A.-C.
    In silico local structure approach: A case study on outer membrane proteins
    Proteins. (2008) 71(1):92-109.

  4. Interview
    Cahier de laboratoire électronique, question(s) de recherche
    Spectra Analysis (2008) 265:46-47.

Year 2007

  1. Etchebest C., Benros C., Bornot A., Camproux A.-C., de Brevern A.G.
    A reduced amino acid alphabet for understanding and designing protein adaptation to mutation
    European Biophysics Journal (2007) 36(8): 1059-69.

  2. Offmann B., Tyagi M., de Brevern A.G.
    Local Protein Structures
    Current Bioinformatics (2007) 2: 165-202.

  3. Bornot A., Offmann B., de Brevern A.G.
    How flexible protein structures are ? New questions on the protein structure plasticity
    Bioforum Europe (2007) 11, 24-25

  4. Doppelt O., Moriaud F., Bornot A., de Brevern A.G.
    Functional annotation strategy for protein structures
    Bioinformation (2007) Mar 19;1(9):357-9.

  5. de Brevern A.G., Etchebest C., Benros C., Hazout S.
    "Pinning strategy": a new approach for predicting the backbone structure in terms of Protein Blocks from sequence
    J Biosci. (2007) 32(1):51-70.

  6. Benros C., Martin J., Tyagi M., de Brevern A.G.
    Description of the local protein structure. I. Classical approaches
    Recent Adv. In Structural Bioinformatics (2007) de Brevern A.G. ed. Research signpost, Trivandrum, India.
    ISBN:978-81-308-0208-4, 1-22

  7. Tyagi M., Benros C., Martin J., de Brevern A.G.
    Description of the local protein structure. II. Classical approaches
    Recent Adv. In Structural Bioinformatics (2007) de Brevern A.G. ed. Research signpost, Trivandrum, India.
    ISBN:978-81-308-0208-4, 23-36

  8. Fuchs P.F.J., Etchebest C., de Brevern A.G.
    Turns prediction
    Recent Adv. In Structural Bioinformatics (2007) de Brevern A.G. ed. Research signpost, Trivandrum, India.
    ISBN:978-81-308-0208-4, 37-56

Year 2006

  1. Benros C., de Brevern A.G, Etchebest C., Hazout S.
    Assessing a novel approach for predicting local 3D protein structures from sequence
    Proteins (2006) 62(4) 865-80

  2. Bornot A., de Brevern A.G
    Protein beta-turn assignments
    Bioinformation (2006) 1(5) 153-5

  3. Gelly J.C., Etchebest C., Hazout S., de Brevern A.G
    Protein Peeling 2: a web server to convert protein structures into series of protein units
    Nucleic Acids Res. (2006) 34(Web Server issue) W75-8

  4. Gelly J.C., de Brevern A.G, Hazout S.
    Protein Peeling: an approach for splitting a 3D protein structure into compact fragments
    Bioinformatics (2006) 22(2) 129-33

  5. Tyagi M., Sharma P., Swamy C.S., Cadet F., Srinivasan N., de Brevern A.G., Offmann B.
    Protein Block Expert (PBE): a web-based protein structure analysis server using a structural alphabet
    Nucleic Acids Res. (2006) 34(Web Server issue) W119-23

  6. Tyagi M., Gowri V.S., Srinivasan N., de Brevern A.G., Offmann B.
    A substitution matrix for structural alphabet based on structural alignment of homologous proteins and its applications
    Proteins (2006) 65(1) 32-9

  7. de Brevern A.G.
    Bioinformatique Structurale
    Habilitation a Diriger des Recherches (2006), 67 pages

Year 2005

  1. de Brevern A.G., Wong H., Tournamille C., Cartron J.-P., Colin Y., Le Van Kim C., Etchebest C.
    A structural model of seven transmembrane helices receptor, Duffy Antigen / Receptor for Chemokines (DARC)
    Biochem Biophys Acta (2005) 1724:288-306.

  2. de Brevern A.G.
    New assessment of a structural alphabet
    In Silico Biology (2005) 5(3):283-9.

  3. Etchebest C.*, Benros C.*, Hazout S.,de Brevern A.G.
    A structural alphabet for local protein structures: improved prediction methods
    Proteins (2005) 59(4), 810 - 827.

  4. Martin J., Letellier G., Marin A., Taly J.-F., de Brevern A.G., Gibrat J.-F.
    Protein secondary structure assignment revisited: a detailed analysis of different assignment methods
    BMC Structural Biology (2005) 5:17.

  5. de Brevern A.G.*, Benros C.*, Hazout S.
    Structural alphabet: from a local point of view to a global description of protein 3D structures
    in Development in Bioinformatics (2005) 127-69

Year 2004

  1. Fourrier L.*, Benros C.*,de Brevern A.G.
    Use of a structural alphabet for analysis of short loops connecting repetitive structures
    BMC Bioinformatics (2004) 5, 58

  2. de Brevern A.G., Benros C., Gautier R., Valadié H., Hazout S., Etchebest C.
    Local backbone structure prediction of proteins
    In Silico Biology (2004) 4, 181-186

  3. de Brevern A.G., Hazout S., Malpertuy A.
    Influence of microarrays experiments missing values on the stability of gene groups by hierarchical clustering
    BMC Bioinformatics (2004) 5, 114

Year 2003

  1. de Brevern A.G., Hazout S.
    'Hybrid Protein Model' for optimally defining 3D protein structure fragments
    Bioinformatics (2003) 19, 345-353

  2. Benros C., de Brevern A.G., Hazout S.
    Hybrid Protein Model (HPM): A Method For Building A Library Of Overlapping Local Structural Prototypes.
    Sensitivity Study And Improvements Of The Training
    Proceedings of IEEE International Workshop on Neural Networks for Signal Processing (2003) 41-57.

Year 2002

  1. de Brevern A.G., Valadié H., Hazout S., Etchebest C.
    Extension of a local backbone description using a structural alphabet. A new approach to the sequence-structure relationship
    Protein Science (2002) 11, 2871-2886

  2. de Brevern A.G., Loirat F., Badel-Chagnon A., André C., Vincens P., Hazout S.
    Genome compartimentation by a Hybrid Chromosome Model (HXM). Application to Saccharomyces cerevisae subtelomeres
    Computers and Chemistry (2002) 26, 437-445

  3. de Brevern A.G.
    Compartimentation génomique
    Biofutur (2002) 225, 20-22

  4. Benros C., Hazout S., de Brevern, A.G.
    "Hybrid Protein Model": a new clustering approach for 3D local structures
    Int. Workshop on Bioinformatics ISMIS (2002) 36-45

  5. de Brevern A.G. , Loirat F., Badel-Chagnon A., Vincens P., Hazout S.
    Genomic compartimentation by a Hybrid Chromosome Model (HXM). Application to Saccharomyces cerevisae subtelomeres
    Troisièmes Journées Ouvertes de Biologie, Informatique et Mathématiques
    in Recueil des Actes (2002) pp.253-256

Year 2001

  1. de Brevern A.G., Hazout S.
    Compacting local protein folds by a "Hybrid Protein Model"
    Theor Chem Acc (2001) 106(1/2), 36-47

  2. Camproux A.C., de Brevern A.G., Hazout S., Tuffery P.
    Exploring the use of a structural alphabet for a structural prediction of protein loops
    Theor Chem Acc (2001) 106(1/2), 28-35

  3. de Brevern A.G., Camproux A.C., Hazout S., Etchebest C., Tuffery P.
    Beyond the secondary structures : the structural alphabets
    in Recent Adv. In Prot. Eng. (2001) 311-318

  4. de Brevern A.G.
    Nouvelles stratégies d'analyses et de prédiction des structures tridimensionnelles des protéines
    Doctorat de l'Université Paris 7 - Spécialité : Analyses de Génomes et Modélisation Moléculaire (2001) 210 pages

  5. de Brevern A.G. , Hazout S.
    Compactage d'une base de données protéiques recodées dans un alphabet structural
    Secondes Journées Ouvertes de Biologie, Informatique et Mathématiques
    in Recueil des Actes (2001) pp.85-92

Year 2000

  1. de Brevern A.G. , Hazout S.
    Hybrid Protein Model (HPM): a method to compact protein 3D-structures information and physicochemical properties
    IEEE - Comp Soc (2000) S1, 49-54

  2. de Brevern A.G. , Etchebest C., Hazout S.
    Bayesian probabilistic approach for predicting backbone structures in terms of protein blocks
    Proteins (2000) 41, 271-287

  3. de Brevern A.G. , Hazout S.
    "Hybrid Protein Model (HPM)" : une nouvelle approche pour caractériser les relations séquence-structure dans les protéines
    Premières Journées Ouvertes de Biologie, Informatique et Mathématiques
    in Recueil des Actes (2000) pp.105-112

Summary

  1. Researcher ID (www.researcherid.com, formely by Thomson Reuters) keeps track of citations and has DOI with links to most publications.

  2. ORCID provides a persistent digital identifier that distinguishes you from every other researcher.

  3. ResearchGate is a social networking site for scientists and researchers to share papers.

  4. the classical Google scholar.

Related works

  1. Craveur P.
    .
    Doctorat de l'Université Paris Diderot - Paris 7 - Spécialité : Bioinformatique Structurale (2014) 2xx p.

  2. Joseph A.P.
    Comparison of protein folds based on similarities in local backbone conformation.
    Doctorat de l'Université Paris Diderot - Paris 7 - Spécialité : Analyses de Génomes et Modélisation Moléculaire (2011) 244 p.

  3. Bornot A.
    Analyse et prédiction de la relation séquence – structure locale et flexibilité au sein des protéines globulaires.
    Doctorat de l'Université Paris Diderot - Paris 7 - Spécialité : Analyses de Génomes et Modélisation Moléculaire (2009) 250 p.

  4. Doppelt-Azeroual O.
    Développement d’une nouvelle méthode performante de classification des surfaces protéiques d’interaction.
    Optimisations et extensions du logiciel MED-SuMo.
    Doctorat de l'Université Paris Diderot - Paris 7 - Spécialité : Analyses de Génomes et Modélisation Moléculaire (2009) 182 p.

  5. Tyagi M.
    New perspectives for protein structure analysis and mining using sequences of a structural alphabet
    Doctorat de l'Université de la Réunion, Spécialité : Bioinformatique (2006) 214 p.

  6. Benros C.
    Analyse et prédiction des structures tridimensionnelles locales des protéines
    Doctorat de l'Université Paris 7 - Spécialité : Analyses de Génomes et Modélisation Moléculaire (2005) 215 p.

    * : authors contribute equally to this work.





    Alexandre G. de Brevern
    Last Modification : March 2023
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