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· Picture of the Lab
We are part of the Department of Structural Biology and Chemistry in Institut Pasteur, Paris.
We use experimental techniques such as crystallography and cryo-electron microscopy to visualize at the atomic level the structure of molecules essential to life and to understand their functional properties, especially for
We complement them with computational approaches such as molecular dynamics (atomic models), normal modes dynamics (coarse-grained models) and statistical thermodynamics, in order to go beyond the essentially static pictures given by these methods.
Computational tools allow to make use of the important information contained in massive sequence data of related molecules in the tree of life and help to understand what is essential in their active site structure and how it is modulated.
When possible we study their structure in the context of their partners in larger macromolecular complexes and try to dissect the molecular interactions between them
in order to understand possible emerging collective properties (systems biology).
Our main goal is to understand how these molecular machines work at the atomic level so as to design structure-inspired drugs (pharmacology and drug discovery) and re-design their active site(s) to make them accept other substrates (synthetic biology).
Publications on computational methods by year (2009-2021)
-New article by M. Tekpinar on software to calculate correlations between residues from dynamical or sequence data (Ref).
-New article with P. Koehl and H. Orland in J. Phys. Chem. B on an application of the extended dipolar Poisson-Boltzmann formalism to detect simultaneously
druggable pockets in proteins, including those with a hydrophobic character Here.
-New article with P. Koehl and H. Orland in J. Comput. Chem. on the parametrization of Elastic Networks for best Normal Modes Analysis of Large biological Macromolecules
-New article in Phys. Rev. E with P. Koehl and H. Orland on the solution of the unbalanced Optimal Transport Problem with statistical physics methods Here.
-Coarse-grained dynamics of entire viruses such as the Dengue virus (Ref)
-With main authors Patrice Koehl (UC Davis) and Henri Orland (CEA, Saclay), a new look at
Optimal Transport theory using the tools of statistical mechanics, just published in Physical Review Letters
(PRL) and Phys Rev E (PRE).
See articles here, PRL.pdf and PRE.pdf.
-Co-organization of a CECAM Meeting on Normal Modes in IHP, Paris, September (Program here).
-New and faster calculations of Normal Modes with Patrice Koehl (Ref).
2017-Simulating the transition path between two known forms of a macromolecule using mixed ENMs,
in J. Chem. Phys. This is a follow-up of our previous MAP method (see also P. Koehl in J. Chem. Phys.)
-Organisation with Y.H. Sanejouand of a one day meeting in Normal Mode analysis and Conformational Transitions in Pasteur (30 May 2017)
-Normal Mode analysis of the dynamics of Zika and Dengue virus capsids (Ref)
-Non-local electrostatics made local (Ref)
-Using AquaSol to investigate the stability of microfibrils (Ref)
-A web site and software to analyze SAXS data and fit them to molecular models by Fred Poitevin et al. in NAR web site issue.
-A meeting in I. Pasteur (Paris) was organized in the framework of our France-Stanford exchange Program
-AquaSol full description (Ref)
-The AquaSol model was extended to include solvent-solvent interactions in PRL, see Recomm by F1000.
The following web sites provide online servers for algorithms such as normal mode
calculation, structural refinement, solvation, mutation and (later) transition path calculation.
a web-based software to calculate SAXS spectra from PDB coordinates,
including the solvent density predicted by AquaSol, see Ref. here.
MinActionPath (MAP) web server can be used to generate the most probable trajectory between two known structural forms
of the same macromolecule (see Ref. here).
The algorithm was greatly accelerated by P. Koehl, as described here.
Go to Older web site for more details on the group activities before 2009.