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Gaillard Thomas
MAITRE DE CONFÉRENCES

Contact

Bureau : 3:30-14
Téléphone : +33169334862
Département/Laboratoire/Service : CA/DER/DEP/BIO
Fonctions complémentaires :
PERSONNEL DE RECHERCHE

Bibliographie & travail en cours

Mission: 

enseignant et chercheur

Biographie: 
2009 - present Assistant professor at the École Polytechnique, Laboratoire de Biochimie
2008 - 2009 Postdoctoral stay at Rutgers University, BioMaPS Institute for Quantitative Biology
2008 French qualification to assistant professor functions, in chemistry and molecular biology (sections 31, 32, and 64)
2007 - 2008 Acting assistant professor (ATER), at Université Louis Pasteur
2004 - 2007 Ph.D. in theoretical biochemistry, Université Louis Pasteur, Strasbourg, France
2003 - 2004 M.Sc. in organic chemistry, Université Pierre et Marie Curie, Paris, France
2003 - 2004 École Nationale Supérieure de Chimie de Paris
2000 - 2004 École Polytechnique (X2000)
1998 - 2000 Scientific preparatory classes, Lycée du Parc, Lyon, France
1998 Baccalaureate
Enseignement: 
  • Biologie Computationnelle (BIO566), École Polytechnique 3rd year
  • Projet en Bioinformatique (BIO/INF588), École Polytechnique 3rd year
  • Bioinformatique Structurale (BIO651A), Master 2 "Engineering and Chemistry of Biomolecules"
  • Utilisation des Outils d'Analyse des Séquences (BIO664), Master 2 "Engineering and Chemistry of Biomolecules"
Recherche: 

Themes

  • Computational protein design
  • Protein sidechain conformation prediction
  • Nucleic acids modeling
  • Infrared spectra calculation
  • Mechanics, dynamics and inhibition of integrins

Methods

  • Molecular mechanics force fields
  • Normal mode analysis
  • Molecular dynamics
  • Quantum chemistry
  • Sequence alignment
  • Homology modeling
  • Molecular docking

Publications et Liens

Publications: 

Articles in peer-reviewed journals

  • Full protein sequence redesign with an MMGBSA energy function.
    T. Gaillard*, T. Simonson*
    Journal of Chemical Theory and Computation, 2017, 13, 4932-4943.
    doi:10.1021/acs.jctc.7b00202
  • PSSweb: protein structural statistics web server.
    T. Gaillard*, R.H. Stote, A. Dejaegere
    Nucleic Acids Research, 2016, 44, W401-W405.
    doi:10.1093/nar/gkw332
  • Protein side chain conformation predictions with an MMGBSA energy function.
    T. Gaillard*, N. Panel, T. Simonson*
    Proteins, 2016, 84, 803-819.
    doi:10.1002/prot.25030
  • Far infrared spectra of solid state L-serine, L-threonine, L-cysteine, and L-methionine in different protonation states
    T. Gaillard, A. Trivella, R.H. Stote, P. Hellwig*
    Spectrochimica Acta A, 2015, 150, 301-307.
    doi:10.1016/j.saa.2015.05.031
  • Pairwise decomposition of an MMGBSA energy function for computational protein design.
    T. Gaillard*, T. Simonson*
    Journal of Computational Chemistry, 2014, 35, 1371-1387.
    doi:10.1002/jcc.23637
  • Computational protein design: the Proteus software and selected applications.
    T. Simonson*, T. Gaillard, D. Mignon, M. Schmidt am Busch, A. Lopes, N. Amara, S. Polydorides, A. Sedano, K. Druart, G. Archontis
    Journal of Computational Chemistry, 2013, 34, 2472-2484.
    doi:10.1002/jcc.23418
  • Protein structural statistics with PSS.
    T. Gaillard*, B.B.L. Schwarz, Y. Chebaro, R.H. Stote, A. Dejaegere*
    Journal of Chemical Information and Modeling, 2013, 53, 2471-2482.
    doi:10.1021/ci400233j
  • Evaluation of DNA force fields in implicit solvation.
    T. Gaillard, D.A. Case*
    Journal of Chemical Theory and Computation, 2011, 7, 3181-3198.
    doi:10.1021/ct200384r
  • Far infrared spectra of solid state aliphatic amino acids in different protonation states.
    A. Trivella, T. Gaillard, R.H. Stote, P. Hellwig*
    Journal of Chemical Physics, 2010, 132, 115105.
    doi:10.1063/1.3356027
  • Dynamics of β3 integrin I-like and Hybrid domains: insight from simulations on the mechanism of transition between open and closed forms.
    T. Gaillard, A. Dejaegere*, R.H. Stote*
    Proteins, 2009, 76, 977-994.
    doi:10.1002/prot.22404
  • Allylic alkylation and ring-closing metathesis in sequence: a successful cohabitation of Pd and Ru.
    C. Kammerer, G. Prestat*, T. Gaillard, D. Madec, G. Poli*
    Organic Letters 2008, 10, 405-408.
    doi:10.1021/ol702694v
  • Comparative normal mode analysis of LFA-1 integrin I domains.
    T. Gaillard, E. Martin, E. San Sebastian, F.P. Cossío, X. Lopez, A. Dejaegere*, R.H. Stote*
    Journal of Molecular Biology, 2007, 374, 231-249.
    doi:10.1016/j.jmb.2007.07.006

Book chapters

  • The inverse protein folding problem: protein design and structure prediction in the genomic era.
    M. Schmidt am Busch, A. Lopes, D. Mignon, T. Gaillard, T. Simonson
    in J. Zeng, R. Zhang, H. Treutlein (Ed.), Quantum Simulations of Materials and Biological Systems.
    Springer Verlag, New York, 2012.
  • Les énergies renouvelables.
    T. Gaillard, J. Berthiaud, M. Depriester
    in S. Hauger (Ed.), L'environnement à la croisée des savoirs.
    Vuibert, Paris, 2009.

Conference proceedings

  • Computational protein design in the genomic era.
    T. Gaillard, M. Schmidt am Busch, A. Lopes, D. Mignon, T. Simonson
    Actes des Journées Ouvertes en Biologie, Informatique et Mathématiques, 2013, 151-158.
    1-4 July 2013, Toulouse, France.
  • Temperature dependence of the far infrared signature of internal hydrogen bonds in proteins as probed for integrins.
    A. Trivella, Y. El Khoury, T. Gaillard, R.H. Stote, N. Merino, F.J. Blanco, P. Hellwig
    5th International Workshop on Infrared Microscopy and Spectroscopy with Accelerator Based Sources
    13-17 September 2009, Banff, Alberta, Canada.
    AIP Conference Proceedings, 2010, 1214, 3-6.
    doi:10.1063/1.3326344

Conference oral communications

  • Computational protein design with an MMGBSA energy function.
    T. Gaillard, N. Panel, D. Mignon, T. Simonson
    International Society of Quantum Biology and Pharmacology (ISQBP) President's Meeting
    19-22 June 2016, Bergen, Norway.
  • Computational protein design with an MMGBSA energy function.
    T. Gaillard, N. Panel, T. Simonson
    XIXe congrès du Groupe de Graphisme et Modélisation Moléculaire (GGMM 2015)
    25-28 May 2015, Sète, France.
  • Computational protein design, implementation and applications.
    T. Gaillard, M. Schmidt am Busch, A. Lopes, D. Mignon, T. Simonson
    Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM 2013)
    1-4 July 2013, Toulouse, France.
  • Évaluation des champs de force d'ADN en solvatation implicite.
    T. Gaillard, D.A. Case
    Journées Modélisation ENS-ENSCP
    3-4 June 2010, Paris, France.
  • Dynamique des domaines βA et hybride des intégrines.
    T. Gaillard, A. Dejaegere, R.H. Stote
    XVe congrès du Groupe de Graphisme et Modélisation Moléculaire (GGMM 2007)
    2-4 May 2007, Autrans, France.
  • Normal mode analysis of the integrin I domain of LFA-1:
    low frequency vibrational contribution to the activation mechanism.

    T. Gaillard, A. Dejaegere, R.H. Stote
    1er Congrès International de Modélisation Moléculaire (CIMM 2005)
    23-25 November 2005, Casablanca, Morocco.

Conference poster communications

  • PSSweb: protein structural statistics web server.
    T. Gaillard, R.H. Stote, A. Dejaegere
    XXe congrès du Groupe de Graphisme et Modélisation Moléculaire (GGMM 2017)
    9-11 May 2017, Reims, France.
  • Design computationnel de protéines, implémentation et applications.
    T. Gaillard, N. Panel, D. Mignon, A. Aleksandrov, T. Simonson
    XVIIIe congrès du Groupe de Graphisme et Modélisation Moléculaire (GGMM 2013)
    21-23 May 2013, Saint Pierre d'Oléron, France.
  • PSS – a protein structural statistics program.
    T. Gaillard, B.B.L. Schwarz, Y. Chebaro, A. Dejaegere
    International Society of Quantum Biology and Pharmacology (ISQBP) President's Meeting
    17-20 June 2012, Stockholm, Sweden.
  • Évaluation des champs de force d'ADN en solvatation implicite.
    T. Gaillard, D.A. Case
    XVIIe congrès du Groupe de Graphisme et Modélisation Moléculaire (GGMM 2011)
    30 May-1st June 2011, La Rochelle, France.
  • Evaluation of DNA force fields in implicit solvation.
    T. Gaillard, D.A. Case
    CECAM workshop “Dynamics and Thermodynamics of Biomolecular Recognition”
    5-7 May 2011, Palaiseau, France.
  • Evaluation of DNA force fields in implicit solvation.
    T. Gaillard, D.A. Case
    International Society of Quantum Biology and Pharmacology (ISQBP) President's Meeting
    13-17 June 2010, Cetraro, Italy.
  • Extension de la partie extracellulaire complète de l'intégrine αVβ3.
    T. Gaillard, A. Dejaegere, R.H. Stote
    XVIe congrès du Groupe de Graphisme et Modélisation Moléculaire (GGMM 2009)
    5-7 May 2009, Mittelwihr, France.
  • Dynamics of β3 integrin I-like and Hybrid domains.
    T. Gaillard, A. Dejaegere, R.H. Stote
    21st Annual Rutgers-UMDNJ Molecular Biophysics Minisymposium (2009)
    29 April 2009, Piscataway, New Jersey.
    poster prize winner
  • Extension of the complete ectodomain of the αVβ3 integrin.
    T. Gaillard, A. Dejaegere, R.H. Stote
    International Society of Quantum Biology and Pharmacology (ISQBP) President's Meeting
    8-13 June 2008, Ascona, Switzerland.
  • Normal mode analysis of LFA-1 integrin I domain.
    T. Gaillard, A. Dejaegere, R.H. Stote
    International Society of Quantum Biology and Pharmacology (ISQBP) President's Meeting
    24-27 June 2006, Strasbourg, France.
Publications HAL: 
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Hal

Publications HAL: 

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