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; Xingyu Chen, postdoc
Ivan Reveguk, Anna Mazurek, Ph.D. students
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 an important research direction in the group. We have
developed the
Proteus software package for physics-based computational protein design.
Proteus software for protein design
Other software and data
Some recent publications
A complete list of recent publications is available here. See also: orcid.org/0000-0002-5117-7338
T. Simonson, editor (2022) Methods in Molecular Biology; Springer Protocols, vol 2405, Computational Peptide Science (book, 424 pages)
E. Michael & T. Simonson (2022) Current Opinion in Structural Biology 72, 46-54. How much can physics do for protein design?
V. Opuu, G. Nigro, T. Gaillard, E. Schmitt, Y. Mechulam & T. Simonson (2020) PLoS Computational Biology, 16, e1007600. Adaptive landscape flattening allows the design of both enzyme:substrate binding and catalytic power.
N. Panel, F. Villa, E. J. Fuentes & T. Simonson (2018) Biophysical Journal, 114, 1091-1102. Accurate PDZ-peptide binding specificity with additive and polarizable free energy simulations.
Teaching material
Other interesting links: