Thomas Gaillard

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Publications and communications

Articles in peer-reviewed journals

• Cryo-EM Structures of Saccharolobus solfataricus Initiation Complexes with Leaderless mRNAs Highlight Archaeal Features and Eukaryotic Proximity.
  G. Bourgeois, P.-D. Coureux, C. Lazennec-Schurdevin, C. Madru, T. Gaillard, M. Duchateau, J. Chamot-Rooke, S. Bourcier, Y. Mechulam^*, E. Schmitt^*
  Nature Communications, 2024, in press.
  
• Physics-Based Computational Protein Design: An Update.
  D. Mignon, K. Druart, E. Michael, V. Opuu, S. Polydorides, F. Villa, T. Gaillard, N. Panel, G. Archontis, T. Simonson^*
  Journal of Physical Chemistry A, 2020, 124, 10637-10648.
  doi:10.1021/acs.jpca.0c07605
• Adaptive Landscape Flattening Allows the Design of Both Enzyme:Substrate Binding and Catalytic Power.
  V. Opuu, G. Nigro, T. Gaillard, E. Schmitt, Y. Mechulam, T. Simonson^*
  PLOS Computational Biology, 2020, 16, e1007600.
  doi:10.1371/journal.pcbi.1007600
• Evaluation of AutoDock and AutoDock Vina on the CASF-2013 Benchmark.
  T. Gaillard^*
  Journal of Chemical Information and Modeling, 2018, 58, 1697-1706.
  doi:10.1021/acs.jcim.8b00312
• 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

• Transition state-based computational enzyme design.
  T. Gaillard, T. Simonson
  in F. Pazos (Ed.), Methods in Molecular Biology: Protein Design and Evolution.
  Humana, New York, 2024.
• 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
  5^th 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 President's Meeting (ISQBP 2016)
  19-22 June 2016, Bergen, Norway.
• Computational protein design with an MMGBSA energy function.
  T. Gaillard, N. Panel, T. Simonson
  XIX^e 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
  XV^e 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
  1^er Congrès International de Modélisation Moléculaire (CIMM 2005)
  23-25 November 2005, Casablanca, Morocco.

Conference poster communications

• Evaluation of AutoDock and AutoDock Vina on the CASF-2013 Benchmark.
  T. Gaillard
  XXII^e congrès du Groupe de Graphisme et Modélisation Moléculaire (GGMM 2021)
  29 September-1^st October 2021, Villeneuve d'Ascq, France.
• Evaluation of AutoDock and AutoDock Vina on the CASF-2013 Benchmark.
  T. Gaillard
  International Society of Quantum Biology and Pharmacology President's Meeting (ISQBP 2021)
  29 June-1^st July 2021, Strasbourg, France.
• Affinity Predictions of PDZ-Peptide Complexes.
  R. Rakotoharisoa, T. Gaillard
  XXI^e congrès du Groupe de Graphisme et Modélisation Moléculaire (GGMM 2019)
  3-5 April 2019, Nice, France.
• Computational protein design with an MMGBSA energy function.
  T. Gaillard, N. Panel, D. Mignon, T. Simonson
  International Society of Quantum Biology and Pharmacology President's Meeting (ISQBP 2018)
  19-21 June 2018, Barcelona, Spain.
• PSSweb: protein structural statistics web server.
  T. Gaillard, R.H. Stote, A. Dejaegere
  XX^e 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
  XVIII^e 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 President's Meeting (ISQBP 2012)
  17-20 June 2012, Stockholm, Sweden.
• Évaluation des champs de force d'ADN en solvatation implicite.
  T. Gaillard, D.A. Case
  XVII^e congrès du Groupe de Graphisme et Modélisation Moléculaire (GGMM 2011)
  30 May-1^st 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 President's Meeting (ISQBP 2010)
  13-17 June 2010, Cetraro, Italy.
• Extension de la partie extracellulaire complète de l'intégrine αVβ3.
  T. Gaillard, A. Dejaegere, R.H. Stote
  XVI^e 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
  21^st 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 President's Meeting (ISQBP 2008)
  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 President's Meeting (ISQBP 2006)
  24-27 June 2006, Strasbourg, France.

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