Thomas Simonson

Professor of Bioinformatics
Ecole Polytechnique
Laboratoire de Biochimie, Biology Department, Palaiseau, France.

Address

Laboratoire de Biochimie, Ecole Polytechnique, 91128 Palaiseau, France

Tel.: +33/1 69 33 38 81. Fax: +33/1 69 33 30 13. Email: thomas.simonson@polytechnique.fr
 

Education:

Graduate of the Ecole Polytechnique, Paris, 1982 (Physics and Mathematics).
Ph.D. (Doctorat de 3ème Cycle, Physics), Université de Paris, 1985.
Habilitation, Université Louis Pasteur, Strasbourg, France, 1993 (Structural Biology).
 

Career:

1985-89: C.N.R.S. Research Scientist (Chargé de Recherche), Laboratoire pour l'Utilisation du Rayonnement Synchrotron, Orsay, France.
1989-92: Associate Research Scientist, Department of Molecular Biophysics and Biochemistry, Yale University, U.S.A.
1992-99: C.N.R.S. Research Scientist (Chargé de Recherche), Institut de Génétique et Biologie Moléculaire et Cellulaire, Strasbourg, France.
1999-2003: C.N.R.S. Senior Research Scientist (Directeur de Recherche), Institut de Génétique et Biologie Moléculaire et Cellulaire, Strasbourg, France.
2000-2003: Director, CNRS Groupement de Recherche 2193, Modélisation et Simulation en Biologie Structurale.
2003-present: Professor of Bioinformatics, Ecole Polytechnique.

10 significant publications (out of a total of 55):

1) T. Simonson (2002) Proc. Nat. Acad. Sci. (USA), 99, 6544-6549. Gaussian fluctuations and linear response in an electron transfer protein.
2) T. Simonson, G. Archontis, M. Karplus (2002) Accts. Chem. Res., 35, 430-437. Protein-ligand recognition: free energy simulations come of age.
3) T. Simonson (2001) Curr. Opin. Struct. Biol., 11, 243-252. Macromolecular electrostatics: continuum models and their growing pains.
4) T. Simonson (2000) Computational Biochemistry and Biophysics (Eds. O. Becker, A. MacKerell, B. Roux, M. Watanabe; Marcel Dekker, New York), Chapter 5, 169-197. Free energy calculations.
5) B. Roux, T. Simonson, Guest Editors (1999) Biophys. Chem., 78, 1-218. Implicit solvent models for biomolecular simulations. Special Issue.
6) G. Archontis, T. Simonson, M. Karplus (2001) J. Mol. Biol., 306, 307-327. Binding free energies and free energy components from molecular dynamics and Poisson-Boltzmann calculations. Application to amino acid recognition by aspartyl-tRNA synthetase.
7) A.T. Brünger, P.D. Adams, W.L. DeLano, P. Gros, R.W. Grosse-Kunstleve, J.-S. Jiang, N.S. Pannu, R.J. Read, L.M. Rice, T. Simonson, (2001) International Tables of Crystallography, Volume F. Editors: M.G. Rossmann and E. Arnold; Dordrecht: Kluwer Academic Publishers, the Netherlands. The structure determination language of the Crystallography and NMR System.
8) A.T. Brünger, P.D. Adams, G.M. Clore, W.L. DeLano, P. Gros, R.W. Grosse-Kunstleve, J.-S. Jiang, J. Kuszewski, M. Nilges, N.S. Pannu, R.J. Read, L.M. Rice, T. Simonson, G.L. Warren (1998) Acta Cryst., D54, 905-921. Crystallography and NMR System (CNS): a new software system for macromolecular structure determination.
9) J. Zeng, M. Fridman, H. Maruta, H. Treutlein, T. Simonson (1999) Prot. Sci., 8, 50-64. Protein-protein recognition: an experimental and computational study of the R89K mutation in Raf and its effect on Ras binding.
10) T. Simonson, D. Perahia, (1995) Proc. Nat. Acad. Sci. (USA), 92, 1082-1086. Internal and interfacial dielectric properties of cytochrome c from molecular dynamics simulations in aqueous solution.
 

Former graduate and post-doctoral advisors:

Françoise Dénoyer, Arnaud Ducruix, Gérard Bricogne, Axel Brünger.
 

List of collaborators:

Guillaume Launay, Josseline Noirel, Alexey Aleksandrov, Anne Lopes, Ph.D. students. Damien Thompson, postdoctoral fellow. Eric Madigou, engineer.
 

Graduate and post-doctoral advisees:

Graduate students (Masters):
Stéphane Prunière, 1995-96
François Wagner, 1997-98
Francesca Maglia, 1999-2000
Estelle Calvez, 2003
Christophe Haberkorn, 2003.
Ph.D student:
Nicolas Calimet, 1997- 2002
Postdoctoral fellows:
Karen Flanagan, 1995-96, Research Scientist, Oxford Molecular Inc., Great Britain.
Jun Zeng, 1996-98, Research Scientist, Cytopia Pty Ltd., Australia.
Siegfried Hoefinger, 1998-99, Postdoctoral Fellow, University of Vienna, Austria.
Mafalda Nina, 1997-99, Research Scientist, Syngenta, Basel, Switzerland.
 

Research contracts:

CNRS, Programme Modélisation et Simulation Numérique, 1998
CNRS, Financement Jeune Equipe, 1999
CNRS, Programme Physique et Chimie du Vivant, 2000-2001
Ministère de la Recherche, ACI Physico-chimie de la Matière Complexe, 2001-2002
Ministère de la Recherche, ACI Bioinformatique, 2002-2003

CNRS-National Science Foundation (USA) (with Scripps Research Institute), 2002-2004

         Ministère de la Recherche, ACI IMPBio, 2004-2006
         CEA/CNRS, Programme Toxicologie Nucléaire, 2004-2006