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
Alexey
Aleksandrov, Research Scientist, CNRS
Thomas
Gaillard, Lecturer, Ecole Polytechnique
Thomas Simonson, Senior Research Scientist, CNRS
David
Mignon, software engineer.
Karen Druard, Audrey Sedano graduate
students.
Savvas Polydorides, Zoltan Palmai, postdoctoral
fellows.
Teaching material
Available software and data
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
M. Schmidt am Busch, A. Sedano & T. Simonson (2010) PLOS One, 5, article e10410. Computational protein design: validation and possible relevance as a tool for homology searching and fold recognition. (Abstract)
A. Aleksandrov, S. Polydorides, G. Archontis & T. Simonson (2010) Journal of Physical Chemistry B, 114, 10634-10648. Predicting the acid/base behavior of proteins: a constant-pH Monte Carlo approach with Generalized Born solvent. (Abstract)
T. Gaillard, A. Dejaegere & R. Stote (2009) Proteins, 76, 977-994. Dynamics of beta 3 integrin I-like and Hybrid domains: Insight from simulations on the mechanism of transition between open and closed forms. (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 complete list of recent publications is available here.
Other interesting links: