Personnel de l'université

Bernard OFFMANN

Professeur des Universités

Coordonnées

Université de Nantes Faculté des Sciences et Techniques Unité Fonctionnalité et Ingénierie des Protéines (UFIP) - UMR CNRS 6286 2, rue de la Houssinière, BP 92208 44322 Nantes Cedex 3, France Tel : +33 (0)2 5112 5721

Bureau
Bureau 002 - Bât 25
Tél
0251125721 (n° interne : 455721)
Fax
33 (0)2 5112 5722
Téléphone 2
+33 (0)2 5112 5721
Télécopie 2
33 (0)2 5112 5722
Mail
Bernard.Offmann@univ-nantes.fr
Site internet
http://www.bernardoffmann.fr

Discipline(s) enseignée(s)

Biochimie, Biologie moléculaire, Bioinformatique structurale

Thèmes de recherche

Bioinformatique structurale

  • Relation séquence-structure-fonction
  • Méthodes en bioinformatique pour l'analyse des structures des protéines
  • Approches en bioinformatique pour l'ingénierie des protéines

Activités / CV

Membre de l'équipe 1 Protein Design In-Silico de l'unité Fonctionnalité et Ingénierie des Protéines (UMR CNRS 6286)
 

Pour une liste complète de publications : cliquer ici

 

Publications récentes

 

2014

 

2013

 

2011

 

2010

 

2009

 

2008


  1. Magali Berland, Bernard Offmann, Isabelle André, Magali Remaud-Siméon and Philippe Charton. A web-based tool for rational screening of mutants libraries using ProSAR. Protein Engineering Design and Selection, In press (2014), doi:10.1093/protein/gzu035.

  2. Manoharan Malini, Fuchs Patrick F., Ramanathan Sowdhamini, Bernard Offmann. Insights on pH-dependent conformational changes of mosquito odorant binding proteins by molecular dynamics simulations. Journal of Biomolecular Structure & Dynamics (2014), 32(11):1742-51. DOI:10.1080/07391102.2013.834118

  3. Swapnil Mahajan, Alexandre G. de Brevern, Bernard Offmann and Narayanaswamy Srinivasan. Correlation between local structural dynamics of proteins inferred from NMR ensembles and evolutionary dynamics of homologues of known structure. Journal of Biomolecular Structure & Dynamics (2014), 32(5):751-758.

  4. Swapnil Mahajan, Garima Agarwal, Mohammed Iftekhar, Bernard Offmann, Alexandre G. de Brevern and Narayanaswamy Srinivasan. DoSA: Database of Structural Alignments. Database (2013). [IF = 2.07]

  5. MANOHARAN Malini*, KANNAN Sankar*, OFFMANN Bernard, Sowdhamini Ramanathan. Association of putative members to family of mosquito odorant binding proteins: Scoring scheme using Fuzzy Functional Templates and Cys residue positions. Bioinformatics and Biology Insights (2013), 7:231-251. doi: 10.4137/BBI.S11096 [IF = 1.809 (unofficial)]

  6. Malini Manoharan, Ng Fuk Chong Matthieu, Aurore Vaïtinadapoulé, Etienne Frumence, Sowdhamini Ramanathan and Bernard Offmann. Comparative genomics of odorant binding proteins in Anopheles gambiae, Aedes aegypti and Culex quinquefasciatus. Genome Biol Evol (2013), 5(1):163-180. [IF = 4.68]

  7. Chandra Sekhar Reddy Chilamakuri, Adwait Joshi, Sane Sudha Rani, Bernard Offmann, and R. Sowdhamini. Cross-Genome Comparisons of Newly Identified Domains in Mycoplasma gallisepticum and Domain Architectures with Other Mycoplasma species. Comparative and Functional Genomics, Volume 2011, Article ID 878973, 13 pages, (2011) - PDF [IF = 1.28]

  8. Agnel Praveen Joseph, Garima Agarwal, Swapnil Mahajan, Jean-Christophe Gelly, Lakshmipuram S. Swapna, Bernard Offmann, Frédéric Cadet, Aurélie Bornot, Manoj Tyagi and Hélène Valadié, et al. A short survey on protein blocks. Biophysical Reviews (2010) 2(3):137-145

  9. Chandra Sekhar Reddy Chilamakuri, Sane Sudha Rani, Bernard Offmann and R. Sowdhamini. Systematic search for putative new domain families in Mycoplasma gallisepticum genome. BMC Research Notes, (2010) 3:98. - PDF

  10. Groben R, Kaloudas D, Raines C, Offmann B; Maberly S.C, Gontero B. Comparative sequence analysis of CP12, a small protein involved in the formation of a Calvin cycle complex in photosynthetic organisms. Photosynth Res. (2010) 103(3):183-94.- PDF

  11. Protein short loop prediction in terms of a structural alphabet. Tyagi M, Bornot A, Offmann B, de Brevern AG. Comput Biol Chem. (2009) 33(4):329-33.

  12. Analysis of loop boundaries using different local structure assignment methods. Tyagi M, Bornot A, Offmann B, de Brevern AG. Protein Sci. 2009 Sep;18(9):1869-81.

  13. Sankaran Sandhya, Saane Sudha Rani, Barah Pankaj, Madabosse Kande Govind, Bernard Offmann, Narayanaswamy Srinivasan, R. Sowdhamini. Length variations amongst protein domain superfamilies and consequences on structure and function. PLoS One,2009, 4(3):e4981. PDF

  14. Thangudu RR, Manoharan M, Srinivasan N, Cadet F, Sowdhamini R, Offmann B: Analysis on conservation of disulphide bonds and their structural features in homologous protein domain families. BMC Struct Biol 2008, 8(1):55. PDF

  15. Chilamakuri CS Reddy, Shameer, K, Offmann, B and Sowdhamini, R. PURE: A webserver for the Prediction of domains in Unassigned Regions in proteins. BMC Bioinformatics, 9(1):281, 2008. PDF

  16. Sandhya S, Pankaj B, Govind MK, Offmann B, Srinivasan N, Sowdhamini R. CUSP: an algorithm to distinguish structurally conserved and unconserved regions in protein domain alignments and its application in the study of large length variations. BMC Struct Biol vol. 8 (1) pp. 28, 2008. PDF

  17. Tyagi M., de Brevern A.G., Srinivasan N., Offmann B. Protein structure mining using a structural alphabet, Proteins 71:920–937, 2008. PDF

Informations complémentaires

Communications

  1. Mahajan S, De Brevern A, Offmann B, Srinivasan N. 2013. Correlation between local structural dynamics of proteins inferred from NMR ensembles and evolutionary dynamics of homologues of known structure. International conference on biomolecular forms and function, Bangalore, India, 06-09 January 2013.

  2. Magali Berland, Philippe Charton, Magali Remaud-Siméon, Bernard Offmann. Protein Sequence activity Relationship pour l’évolution dirigée des enzymes. Colloque du GDR 2825 « Nouvelles approches en Evolution Dirigée des Protéines », Ax-les-thermes, 10-11 Octobre 2011.

  3. Magali Berland, Philippe Charton, Magali Remaud-Siméon, Bernard Offmann. ProSAR: Implementation and assessment of an approach based on a genetic algoritm toward directed evolution of enzymes. Congrès de la SFBBM (Société Française de Biochimie et Biologie Moléculaire), Ax-les-thermes, 12-14 Octobre 2011.

  4. Magali Berland, Bernard Offmann, Isabelle André, Magali Remaud-Siméon et Philippe Charton. Prediction of enzyme activity: Implementation of the ProSAR method and assessment on experimental dataset from different sources. 2nd symposium for Protein Engineering for Biocatalysis, Greifswald, Allemagne, 29-31 Aout 2012.

  5. Frédéric Cadet, Bernard Offmann. A Novel Computational Approach for Engineering Enzymes for Better Performance : Case of the Enantioselectivity of An Epoxide Hydrolase. The 5th Medicinal Biotech Forum, Beijing, China, 7-9 November 2011.

  6. Bernard Offmann, Manoj Tyagi, Frédéric Cadet, N. Srinivasan, Alexandre G. de Brevern. Structural variability of pentapeptides. 5th Indo French Bioinformatics Meeting (IFBM 2011), Hyderabad, 23-25 March 2011.

  7. Manoharan M, Ng Fuk Chong M, Vaitinadapoulle A, Frumence E, Sowdhamini R, and Offmann B. Identification and characterisation of novel atypical odorant binding proteins in the mosquito genomes. 9th European Congress on Computation Biology (ECCB10), Ghent, Belgium, 26-29 September 2010.

  8. Offmann B, Tyagi M, Joseph A, Drula M, Grondin M, Frumence E, Vaitinadapoulle A, Cadet F, Srinivasan N, and de Brevern A. 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), Ghent, Belgium, 26-29 September 2010.

  9. Joseph A.P., Bornot A., Offmann B., Srinivasan N., Tyagi M., Valadié H., Etchebest C., de Brevern A.G. Protein Blocks: from simple structural approximation to multiple applications. Dixième Journées Ouvertes de Biologie, Informatique et Mathématiques (JOBIM 2009), Nantes, France, 9-11 June 2009.

  10. Offmann B., Thangudu T., Tyagi M., de Brevern A.G., Srinivasan N., Sowdhamini R. Bridges and Blocks: A Taste of Protein Structure Analysis in Indo-French collaboration, Third Indo-French Bioinformatics Meeting (IFBM 2006), Bangalore, India, 12-14 June 2006.

  11. Tyagi M., Offmann B., de Brevern A.G., Srinivasan N. Structural Alphabets from Protein Structure Description to Comparison. Third Indo-French Bioinformatics Meeting (IFBM 2006), Bangalore, India, 12-14 June 2006.

  12. Tyagi M., Srinivasan N., de Brevern A.G., Cadet F., Offmann B. Protein Block Expert (PBE): a web server for the encoding and analysis of protein 3D structures in terms of a structural alphabet, German Conference on Bioinformatics (GCB’05), Hamburg, Germany, 5-7 October 2005.

  13. Tyagi M., Gowri V.S., Srinivasan N., de Brevern A.G., Offmann B. Structural alphabet substitution matrix derived from structurally aligned homologous proteins and its applications. 3rd European Conference on Computational Biology (ECCB 2005), Madrid, Spain 28 September-1st October 2005.

  14. Idmont B, Charton P, Ralambondrainy H, Offmann B. Réduction de dimension à l’aide des ondelettes. 11e rencontre de la Société Francaise de Classification, Bordeaux, 8-10 septembre 2004.

  15. Salma Locate, Bénédicte Beylot, Emmanuelle Huitelec, Claude Rouch, Bernard Offmann. Fourier Spectral Analysis of Protein Functional Families. 1st European Conference on Computational Biology (ECCB 2003), Paris, 27-30 September 2003.

  16. Huitelec E, Charton P, Beylot B, Locate S, Rouch C, Offmann B. MutScan, A Fourier Based Method For the Identification of Key Amino Acids in Protein Sequences. 1st European Conference For Computational Biology, Paris, 27-30 September 2003.

  17. Forget L., Hoarau J-Y., Mungur H., Payet J., Badaloo G., Hellmann M., Ramdoyal K., Wong Sak Hoi L., Raboin L.M., Dookun-Saumtally A., Offmann B. Detection of QTAs for agronomic traits across crop-cycles and seasons in two segregating populations. Molecular Biology Workshop of ISSCT, Montpellier, 7-11 April, (2003).

  18. Besnard G., Pinçon G., D’Hont A., Robert C., Rondeau Ph., Hoarau J-Y., Offmann B., Rouch C., Cadet F. Characterization of the phosphoenolpyruvate carboxylase gene family in grasses (Poaceae). Molecular Biology Workshop of ISSCT, Montpellier, 7-11 April, (2003).

  19. Offmann B., Fontaine J-F., Cadet F. BISAR A java tool for the Fourier analysis of biological sequences. Journées Ouvertes Biologie Informatique Mathématiques (JOBIM), Saint Malo, 10-12 Juin 2002.

  20. Besnard G, Offmann B, Robert C, Baret P, Rouch C, Cadet F. Phosphoenolpyruvate carboxylase cDNA phylogeny to investigate the C4 photosynthetic pathway evolution in grasses. Proc XIIth Int Congr Photosynth, Brisbane, Australia, August 2001.

  21. Offmann B., Raboin L.M., Asnaghi C., Kaye C., Ruffel S., Roques D., Girard J.C., Notaise J., Saumtally S., Dookun A., Grivet L., Rott P., Glaszmann J.C., D’Hont A. Progress in genetic analysis of resistance to rust and leaf scald in sugarcane. VIIIth Plant and Animal Genome Annual Congress, San Diego, California, 9-12 January, 2000.


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