Alexandre G de Brevern

Summary

Country: France

Publications

  1. pmc Comparison of tertiary structures of proteins in protein-protein complexes with unbound forms suggests prevalence of allostery in signalling proteins
    Lakshmipuram S Swapna
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India
    BMC Struct Biol 12:6. 2012
  2. pmc PredyFlexy: flexibility and local structure prediction from sequence
    Alexandre G de Brevern
    INSERM, U665, DSIMB, Paris, France
    Nucleic Acids Res 40:W317-22. 2012
  3. doi request reprint Species specific amino acid sequence-protein local structure relationships: An analysis in the light of a structural alphabet
    Alexandre G de Brevern
    Dynamique des Structures et Interactions des Macromolecules Biologiques DSIMB, INSERM, U665, Paris, 6, rue Alexandre Cabanel, F 75015, France
    J Theor Biol 276:209-17. 2011
  4. pmc 3D structural models of transmembrane proteins
    Alexandre G de Brevern
    INSERM UMR S 665, Dynamique des Structures et Interactions des Macromolecules Biologiques DSIMB, Institut National de Transfusion Sanguine INTS, Universite Paris Diderot Paris 7, Paris, France
    Methods Mol Biol 654:387-401. 2010
  5. pmc In silico studies on DARC
    Alexandre G de Brevern
    INSERM UMR S 665, Universite Paris Diderot Paris 7, Institut National de la Transfusion Sanguine, 6, rue Alexandre Cabanel, 75739 Paris 15, France
    Infect Disord Drug Targets 9:289-303. 2009
  6. doi request reprint Cis-trans isomerization of omega dihedrals in proteins
    Pierrick Craveur
    INSERM UMR S 665, Dynamique des Structures et Interactions des Macromolécules Biologiques, Universite Denis Diderot Paris 7, INTS, 6, rue Alexandre Cabanel, 75739 Paris cedex 15, France
    Amino Acids 45:279-89. 2013
  7. doi request reprint Protein Peeling 3D: new tools for analyzing protein structures
    Jean Christophe Gelly
    Dynamique des Structures et Interactions des Macromolécules Biologiques, INSERM UMR S 665, Universite Paris Diderot Paris 7, Paris, France
    Bioinformatics 27:132-3. 2011
  8. pmc A recombinant dromedary antibody fragment (VHH or nanobody) directed against human Duffy antigen receptor for chemokines
    Dorota Smolarek
    INSERM, UMR_S 665, 75015 Paris, France
    Cell Mol Life Sci 67:3371-87. 2010
  9. doi request reprint Analyzing the sequence-structure relationship of a library of local structural prototypes
    Cristina Benros
    Equipe de Bioinformatique Genomique et Moleculaire, INSERM UMR S726, Universite Denis Diderot Paris 7, place Jussieu, Paris, France
    J Theor Biol 256:215-26. 2009
  10. pmc iPBA: a tool for protein structure comparison using sequence alignment strategies
    Jean Christophe Gelly
    INSERM, UMR S 665, Dynamique des Structures et Interactions des Macromolécules Biologiques, Universite Paris Diderot Paris 7, Institut National de la Transfusion Sanguine, 6, rue Alexandre Cabanel, 75739 Paris cedex 15, France
    Nucleic Acids Res 39:W18-23. 2011

Collaborators

Detail Information

Publications33

  1. pmc Comparison of tertiary structures of proteins in protein-protein complexes with unbound forms suggests prevalence of allostery in signalling proteins
    Lakshmipuram S Swapna
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India
    BMC Struct Biol 12:6. 2012
    ..In this work, we have addressed the question "What is the nature, extent, location and functional significance of structural changes which are associated with formation of protein-protein complexes?"..
  2. pmc PredyFlexy: flexibility and local structure prediction from sequence
    Alexandre G de Brevern
    INSERM, U665, DSIMB, Paris, France
    Nucleic Acids Res 40:W317-22. 2012
    ..PredyFlexy can be accessed at http://www.dsimb.inserm.fr/dsimb_tools/predyflexy/...
  3. doi request reprint Species specific amino acid sequence-protein local structure relationships: An analysis in the light of a structural alphabet
    Alexandre G de Brevern
    Dynamique des Structures et Interactions des Macromolecules Biologiques DSIMB, INSERM, U665, Paris, 6, rue Alexandre Cabanel, F 75015, France
    J Theor Biol 276:209-17. 2011
    ..Thus, AAS-PS relationships are species dependent. These results can give useful insights for improving prediction methodologies which take the species specific information into account...
  4. pmc 3D structural models of transmembrane proteins
    Alexandre G de Brevern
    INSERM UMR S 665, Dynamique des Structures et Interactions des Macromolecules Biologiques DSIMB, Institut National de Transfusion Sanguine INTS, Universite Paris Diderot Paris 7, Paris, France
    Methods Mol Biol 654:387-401. 2010
    ..In all cases, the most important factor when proceeding to correct structural models is taking the experimental data into account...
  5. pmc In silico studies on DARC
    Alexandre G de Brevern
    INSERM UMR S 665, Universite Paris Diderot Paris 7, Institut National de la Transfusion Sanguine, 6, rue Alexandre Cabanel, 75739 Paris 15, France
    Infect Disord Drug Targets 9:289-303. 2009
    ..Finally, we present recent development of protein-protein docking between DARC structural models and CXCL-8 structures. We propose a hierarchical search based on separated rigid and flexible docking...
  6. doi request reprint Cis-trans isomerization of omega dihedrals in proteins
    Pierrick Craveur
    INSERM UMR S 665, Dynamique des Structures et Interactions des Macromolécules Biologiques, Universite Denis Diderot Paris 7, INTS, 6, rue Alexandre Cabanel, 75739 Paris cedex 15, France
    Amino Acids 45:279-89. 2013
    ..Cis-trans proline isomerization reactions represents a vast and promising research area that still needs to be further explored for a better understanding of isomerization mechanism and improvement of cis peptide bond predictions. ..
  7. doi request reprint Protein Peeling 3D: new tools for analyzing protein structures
    Jean Christophe Gelly
    Dynamique des Structures et Interactions des Macromolécules Biologiques, INSERM UMR S 665, Universite Paris Diderot Paris 7, Paris, France
    Bioinformatics 27:132-3. 2011
    ..New features include identification of structural domains, detection of unstructured terminal elements and evaluation of the stability of protein unit structures...
  8. pmc A recombinant dromedary antibody fragment (VHH or nanobody) directed against human Duffy antigen receptor for chemokines
    Dorota Smolarek
    INSERM, UMR_S 665, 75015 Paris, France
    Cell Mol Life Sci 67:3371-87. 2010
    ..This first report on a VHH with specificity for a red blood cell protein exemplifies VHHs' potentialities to target, to purify, and to modulate the function of cellular markers...
  9. doi request reprint Analyzing the sequence-structure relationship of a library of local structural prototypes
    Cristina Benros
    Equipe de Bioinformatique Genomique et Moleculaire, INSERM UMR S726, Universite Denis Diderot Paris 7, place Jussieu, Paris, France
    J Theor Biol 256:215-26. 2009
    ..These results are so useful to analyze the sequence-structure relationships, but could also be used to improve fragment-based method for protein structure prediction from sequence...
  10. pmc iPBA: a tool for protein structure comparison using sequence alignment strategies
    Jean Christophe Gelly
    INSERM, UMR S 665, Dynamique des Structures et Interactions des Macromolécules Biologiques, Universite Paris Diderot Paris 7, Institut National de la Transfusion Sanguine, 6, rue Alexandre Cabanel, 75739 Paris cedex 15, France
    Nucleic Acids Res 39:W18-23. 2011
    ..As a fast and efficient 'sequence-based' structure comparison tool, we believe that it will be quite useful to the scientific community. iPBA can be accessed at http://www.dsimb.inserm.fr/dsimb_tools/ipba/...
  11. doi request reprint Progressive structure-based alignment of homologous proteins: Adopting sequence comparison strategies
    Agnel Praveen Joseph
    INSERM, UMR S 665, Dynamique des Structures et Interactions des Macromolécules Biologiques, 6, rue Alexandre Cabanel, 75739 Paris cedex 15, France
    Biochimie 94:2025-34. 2012
    ..Comparison with other rigid-body and flexible MSTAs also indicate that mulPBA alignments are superior to most of the rigid-body MSTAs and highly comparable to the flexible alignment methods...
  12. ncbi request reprint Assessing a novel approach for predicting local 3D protein structures from sequence
    Cristina Benros
    Equipe de Bioinformatique Genomique et Moleculaire, INSERM U726, Universite Denis Diderot Paris 7, Paris, France
    Proteins 62:865-80. 2006
    ..Our approach predicts from sequence alone and will thus provide valuable information for proteins without structural homologs. Candidates will also contribute to global structure prediction by fragment assembly...
  13. doi request reprint Improvement of protein structure comparison using a structural alphabet
    Agnel Praveen Joseph
    INSERM UMR S 665, Dynamique des Structures et Interactions des Macromolécules Biologiques, 6, rue Alexandre Cabanel, 75739 Paris cedex 15, France
    Biochimie 93:1434-45. 2011
    ..The quality of alignment is better than DALI and MUSTANG in 81.3% of the cases. Thus our study has resulted in an impressive improvement in the quality of protein structural alignment...
  14. ncbi request reprint Protein contacts, inter-residue interactions and side-chain modelling
    Guilhem Faure
    Equipe de Bioinformatique Genomique et Moleculaire, Universite Paris Diderot, 75251 Paris, France
    Biochimie 90:626-39. 2008
    ..For instance, the interactions involving Tryptophan greatly decrease...
  15. pmc Local backbone structure prediction of proteins
    Alexandre G de Brevern
    Equipe de Bioinformatique Genomique et Moleculaire, INSERM E03 46, Universite Denis Diderot Paris 7, 75251 Paris, France
    In Silico Biol 4:381-6. 2004
    ..LocPred is a software which allows the users to submit a protein sequence and performs a prediction in terms of PBs. The prediction results are given both textually and graphically...
  16. pmc Fast and automated functional classification with MED-SuMo: an application on purine-binding proteins
    Olivia Doppelt-Azeroual
    INSERM UMR S 665, Dynamique des Structures et Interactions des Macromolecules Biologiques DSIMB, Universite Paris Diderot Paris 7, Institut National de la Transfusion Sanguine INTS, 6, rue Alexandre Cabanel, 75739 Paris cedex 15, France
    Protein Sci 19:847-67. 2010
    ..Applications of this classification by binding mode similarity include target-based drug design and prediction of cross-reactivity and therefore potential toxic side effects...
  17. pmc Cis-trans peptide variations in structurally similar proteins
    Agnel Praveen Joseph
    INSERM UMR S 665, Dynamique des Structures et Interactions des Macromolécules Biologiques, Universite Denis Diderot Paris 7, INTS, 6 rue Alexandre Cabanel, Paris Cedex 15, France
    Amino Acids 43:1369-81. 2012
    ..Cis-trans changes are also seen to facilitate inter-domain and inter-protein interactions. As in the case of folding, cis-trans conversions have been used as an important driving factor in evolution...
  18. pmc A new prediction strategy for long local protein structures using an original description
    Aurélie Bornot
    INSERM UMR S, Universite Paris Diderot, Institut National de la Transfusion Sanguine, France
    Proteins 76:570-87. 2009
    ..Moreover, a confidence index for the direct estimation of prediction quality is proposed. Finally, our method is proved to be very competitive with cutting-edge strategies encompassing three categories of local structure predictions...
  19. doi request reprint Analysis of protein contacts into Protein Units
    Guilhem Faure
    INSERM UMR S 726, Equipe de Bioinformatique Genomique et Moleculaire EBGM, DSIMB, Universite Paris Diderot Paris 7, case 7113, 2 place Jussieu, 75251 Paris, France
    Biochimie 91:876-87. 2009
    ..Moreover, we highlight the preferential amino acid interactions inside and between PUs. Our results show that PUs are clearly an intermediate level between secondary structures and protein structural domains...
  20. pmc Use of a structural alphabet for analysis of short loops connecting repetitive structures
    Laurent Fourrier
    Equipe de Bioinformatique Genomique et Moleculaire, INSERM E0346, Universite Denis Diderot Paris 7, case 7113, 2, place Jussieu, 75251 Paris Cedex 05, France
    BMC Bioinformatics 5:58. 2004
    ..In the present study, we use this structural alphabet to analyze and predict the loops connecting two repetitive structures...
  21. pmc Predicting protein flexibility through the prediction of local structures
    Aurélie Bornot
    INSERM UMR S 665, Dynamique des Structures et Interactions des Macromolecules Biologiques DSIMB, University Paris Diderot, Institut National de Transfusion Sanguine, INTS, 6, rue Alexandre Cabanel, 75739 Paris cedex 15, France
    Proteins 79:839-52. 2011
    ..Accordingly, flexibility information should be taken into account in structural prediction assessments...
  22. doi request reprint Comparative analysis of threshold and tessellation methods for determining protein contacts
    Jeremy Esque
    LPTM, CNRS UMR 8089, Université de Cergy Pontoise, Cergy Pontoise, France
    J Chem Inf Model 51:493-507. 2011
    ..In conclusion, the tessellation method is more accurate because of its fine adaptation to local protein topology, with far-reaching implications for most contact-based prediction methods of protein folding...
  23. pmc Analysis of HSP90-related folds with MED-SuMo classification approach
    Olivia Doppelt-Azeroual
    MEDIT SA, 2 rue du Belvédère, Palaiseau, France
    Drug Des Devel Ther 3:59-72. 2009
    ..The different clusters created by MED-SMA yield interesting observations. For instance, one cluster gathers three types of proteins (HSP90, topoisomerase VI, and BCK) which all bind the drug radicicol...
  24. doi request reprint mulPBA: an efficient multiple protein structure alignment method based on a structural alphabet
    Sylvain Leonard
    a INSERM UMR S 665, DSIMB, 6, rue Alexandre Cabanel, F 75739, Paris, France
    J Biomol Struct Dyn 32:661-8. 2014
    ..Superimposed structures in PDB format can be also downloaded, and the results are quickly obtained. mulPBA server can be accessed at www.dsimb.inserm.fr/dsimb_tools/mulpba/ . ..
  25. pmc β-Bulges: extensive structural analyses of β-sheets irregularities
    Pierrick Craveur
    INSERM, U665, DSIMB, F 75739, Paris, France University of Paris Diderot, Sorbonne Paris Cité, UMR_S 665, F 75739, Paris, France Institut National de la Transfusion Sanguine INTS, F 75739, Paris, France Laboratoire d Excellence GR Ex, F 75739, Paris, France
    Protein Sci 22:1366-78. 2013
    ..Displacement of β-bulges along the sequence was also investigated by Molecular Dynamics simulations. ..
  26. pmc Local structural differences in homologous proteins: specificities in different SCOP classes
    Agnel Praveen Joseph
    INSERM, UMR S 665, Dynamique des Structures et Interactions des Macromolecules Biologiques DSIMB, Paris, France
    PLoS ONE 7:e38805. 2012
    ..These are mainly associated with short loops joining the regular secondary structures that mediate a reversal in the chain direction. Rare β-turns of type I' and II' are also identified as preferred sites for insertions...
  27. pmc Comparative analysis of missing value imputation methods to improve clustering and interpretation of microarray experiments
    Magalie Celton
    INSERM UMR S 726, Equipe de Bioinformatique Genomique et Moleculaire, DSIMB, Universite Paris Diderot Paris 7, 2 place Jussieu, Paris, France
    BMC Genomics 11:15. 2010
    ..In this study, we have evaluated twelve different usable methods, and their influence on the quality of gene clustering. Interestingly we have used several datasets, both kinetic and non kinetic experiments from yeast and human...
  28. doi request reprint Influence of assignment on the prediction of transmembrane helices in protein structures
    Jean Pylouster
    INSERM UMR S 726, Equipe de Bioinformatique Genomique et Moleculaire EBGM, DSIMB, Universite Paris Diderot Paris 7, case 7113, 2, place Jussieu, 75251, Paris, France
    Amino Acids 39:1241-54. 2010
    ..This last result highlights the importance of the correct assignment choice to evaluate the prediction assessment...
  29. doi request reprint Evolution study of the Baeyer-Villiger monooxygenases enzyme family: functional importance of the highly conserved residues
    Joseph Rebehmed
    INSERM, U665, DSIMB, F 75739 Paris, France
    Biochimie 95:1394-402. 2013
    ..These behaviors could explain the enzyme selectivity and specificity for different ligands...
  30. pmc Assignment of PolyProline II conformation and analysis of sequence--structure relationship
    Yohann Mansiaux
    INSERM, UMR S 665, Dynamique des Structures et Interactions des Macromolecules Biologiques DSIMB, Paris, France
    PLoS ONE 6:e18401. 2011
    ..Recent studies have shown that PPII frequency is higher than expected, and they could have an important role in protein-protein interactions...
  31. pmc DoSA: Database of Structural Alignments
    Swapnil Mahajan
    Dynamique des Structures et Interactions des Macromolécules Biologiques, UMR S INSERM S665, Faculté des Sciences et Technologies, Universite de la Reunion, F 97715 Saint Denis Messag Cedex 09, La Reunion, France
    Database (Oxford) 2013:bat048. 2013
    ..Database URL: http://bo-protscience.fr/dosa/..
  32. pmc Selective constraint on human pre-mRNA splicing by protein structural properties
    Jean Christophe Gelly
    INSERM, UMR S 665, Dynamique des Structures et Interactions des Macromolécules Biologiques, Paris, France
    Genome Biol Evol 4:966-75. 2012
    ..Overall, our results suggest that fine-scale protein structural requirements have significant influences on the splicing patterns of human mRNAs...
  33. ncbi request reprint Genome compartimentation by a hybrid chromosome model (HXM). Application to Saccharomyces cerevisae subtelomeres
    Alexandre G de Brevern
    Equipe de Bioinformatique Genomique et Moleculaire, Unité INSERM U436, Universite Denis Diderot Paris 7, Paris, France
    Comput Chem 26:437-45. 2002
    ..The approach HXM is a fast and efficient tool for mapping entire genomes and for extracting ancient duplications within or between genomes...