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
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
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.
V. Opuu, M. Silvert & T. Simonson (2017) Computational design of fully overlapping coding schemes for protein pairs and triplets. Scientific Reports, 7, article 15873.
S. Polydorides, E. Michael, D. Mignon, K. Druart, G. Archontis & T. Simonson (2016) In "Methods in Molecular Biology: Design and Creation of Protein Ligand Binding Proteins", editor: Barry Stoddard. Springer Verlag, New York. Proteus and the design of ligand binding sites. (Invited article)
T. Gaillard, N. Panel & T. Simonson (2016) Proteins 84, 803-819. Protein sidechain conformation predictions with an MMGBSA energy function.
T. Simonson, S. Ye-Lehmann, Z. Palmai, N. Amara, S. Wydau-Dematteis, E. Bigan, K. Druart, C. Moch & P. Plateau (2016) Proteins, 84, 240-53. Redesigning the sterospecificity of tyrosyl-tRNA synthetase.
Other interesting links: