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.
Thomas Simonson, Senior Research Scientist, CNRS
Mignon, software engineer.
Karen Druard, graduate student
Savvas Polydorides, Zoltan Palmai, postdoctoral fellows
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 newer research direction in the group. We have recently developed the Proteus software package and the Proteins@Home distributed computing platform for structure prediction and design.
Proteus software for protein design
Other software and data
Some recent publications
A complete list of recent publications is available here.
T. Gaillard & T. Simonson (2014) Journal of Computational Chemistry 35, 1371-1387. Pairwise Decomposition of an MMGBSA Energy Function for Computational Protein Design.
T. Simonson, T. Gaillard, D. Mignon, M. Schmidt am Busch, A. Lopes, N. Amara, S. Polydorides, A. Sedano, K. Druart & G. Archontis (2013) Journal of Computational Chemistry, 34, 2472-84. Computational protein design: the Proteus software and selected applications.
T. Simonson & P. Satpati (2012) Proteins, 80, 2742-57. Nucleotide recognition by the initiation factor aIF5B: free energy simulations of a neo-classical GTPase.
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)
A. Aleksandrov, D. Thompson & T. Simonson (2010) Journal of Molecular Recognition, 23, 117-127. Alchemical free energy simulations for biological complexes: powerful but temperamental....
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