BIOS Research Group
BIOcomputing
and Structure
We are a part of the
Biochemistry Laboratory
in the Biology Department
of
the Ecole Polytechnique
and the Centre National de la Recherche
Scientifique.
We are located in the Ecole
Polytechnique, Palaiseau, just outside of Paris.
snail-mail: Laboratoire de Biochimie, Ecole
Polytechnique, 91128 Palaiseau, France.
People
Thomas
Simonson, Senior Research Scientist, CNRS.
Thomas
Gaillard, Lecturer, Ecole Polytechnique
David
Mignon, software engineer.
Najette Amara, Audrey Sedano Ph.D.
students.
Priyadarshi Satpati, postdoctoral fellow.
Teaching material
Available software
Research interests
Our group uses computer modeling and simulation to study and to
engineer structure-function relationships in biomolecules. We use
state-of-the-art simulation techniques, including computational
protein design, molecular dynamics, continuum electrostatics, and
free energy perturbation techniques, and a significant portion of our
effort is directed at the development of new techniques as new needs
arise. We are especially interested in protein engineering,
protein-ligand recognition, and the inverse protein folding problem.
We have taken part for many years in the development of free energy
perturbation techniques for proteins, and these techniques are now
maturing into a reliable and remarkable tool. Recent applications to
aminoacyl-tRNA synthetases have provided insights into the
translation of the genetic code. Protein design using directed
evolution is a new research direction in the group. We have recently
developed the Proteins@Home
distributed computing platform for structure prediction and design.
Some recent publications
D. Thompson, C. Lazennec, P. Plateau & T.
Simonson (2007) Journal of Biological
Chemistry, 282,
30856-30868.
Ammonium scanning in an enzyme active site: the
chiral specificity of aspartyl-tRNA synthetase. (Abstract)
M. Schmidt am Busch, A. Lopes, D. Mignon &
T. Simonson (2008) Journal of Computational
Chemistry, 29,
1092-1102.
Computational protein design: software implementation,
parameter optimization, and performance of a simple method.
(Abstract)
M. Schmidt am Busch, D. Mignon &
T. Simonson (2009) Proteins, 77,
139–158.
Computational
protein design as a tool for fold recognition. (Abstract)
A. Aleksandrov, L.
Schuldt, W. Hinrichs & T. Simonson (2008) Journal
of Molecular Biology, 378,
896-910.
Tet repressor induction by tetracycline: a molecular
dynamics, continuum electrostatics, and crystallographic study.
(Abstract)
G. Launay & T. Simonson (2008) BMC Bioinformatics, 9, 427-443. Homology modelling of protein-protein complexes: a simple method and its possibilities and limitations. (Abstract)
A. Alexandrov &
T. Simonson (2008) Journal of the
American Chemistry Society, 130,
1114-1115.
Molecular dynamics simulations of the 30S ribosomal
subunit reveal a preferred tetracycline binding site. (Abstract)
J. Noirel & T. Simonson (2008) Journal of Chemical Physics, 129, 185104-185112. Neutral evolution of proteins: the superfunnel in sequence space and its relation to mutational robustness. (Abstract)
A complete list of recent publications is available here.
Other interesting links: