Research Topics
| Alexandre G de BrevernSummaryCountry: France Publications
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Detail Information
Publications
PredyFlexy: flexibility and local structure prediction from sequenceAlexandre 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/...
Species specific amino acid sequence-protein local structure relationships: An analysis in the light of a structural alphabetAlexandre 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...- 3D structural models of transmembrane proteinsAlexandre 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... - In silico studies on DARCAlexandre 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... - Protein Peeling 3D: new tools for analyzing protein structuresJean 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..AVAILABILITY: The website is free and open to all users with no login requirements at http://www.dsimb.inserm.fr/dsimb-tools/peeling3... - iPBA: a tool for protein structure comparison using sequence alignment strategiesJean 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/... - A recombinant dromedary antibody fragment (VHH or nanobody) directed against human Duffy antigen receptor for chemokinesDorota 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... - Analyzing the sequence-structure relationship of a library of local structural prototypesCristina 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... - Progressive structure-based alignment of homologous proteins: Adopting sequence comparison strategiesAgnel 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... 
Assessing a novel approach for predicting local 3D protein structures from sequenceCristina 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...- Improvement of protein structure comparison using a structural alphabetAgnel 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... - Local backbone structure prediction of proteinsAlexandre 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... - Protein contacts, inter-residue interactions and side-chain modellingGuilhem 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... - Fast and automated functional classification with MED-SuMo: an application on purine-binding proteinsOlivia 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... - Cis-trans peptide variations in structurally similar proteinsAgnel 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... - A new prediction strategy for long local protein structures using an original descriptionAurélie 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... - Analysis of protein contacts into Protein UnitsGuilhem 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... - Use of a structural alphabet for analysis of short loops connecting repetitive structuresLaurent 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... - Predicting protein flexibility through the prediction of local structuresAurélie 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... - Comparative analysis of threshold and tessellation methods for determining protein contactsJeremy 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... - Analysis of HSP90-related folds with MED-SuMo classification approachOlivia 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... - Local structural differences in homologous proteins: specificities in different SCOP classesAgnel 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... - Comparative analysis of missing value imputation methods to improve clustering and interpretation of microarray experimentsMagalie 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... - Influence of assignment on the prediction of transmembrane helices in protein structuresJean 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... - Assignment of PolyProline II conformation and analysis of sequence--structure relationshipYohann 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... - Selective constraint on human pre-mRNA splicing by protein structural propertiesJean 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... - Genome compartimentation by a hybrid chromosome model (HXM). Application to Saccharomyces cerevisae subtelomeresAlexandre G de Brevern
, , , 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...