· Introduction/News

- Servers
· NOMAD-Ref server
· PDB_Hydro server
· MinActionPath server
· AquaSAXS server
· Job queue status

· References
· Homes & Links

· Main site

· Google Scholar



Ligand-gated ion channels

-Structural basis for the gating mechanism in GLIC (PNAS, Dec 2013), see also Q & A
-Structural basis for ion permeation in GLIC (EMBO Journal, Jan 2013) at 2.4 Angstrom
-Structural basis for alcohol potentiation in GLIC (Nature Comm., April 2013)

DNA polymerases

- Snapshots of Terminal deoxynucleotidyl transferase caught in action: dynamical aspects of the two-metal-ion mechanism (J. Gouge et al., J. Mol. Biol., Jul 2013)
- A movie illustrating the catalytical cycle of Tdt, made by Jerome Gouge, can be found here in Quicktime format.
- Structures of inhibitors of Tdt, with G. Maga (Milan) and R. di Santo (Roma), J. Med. Chem., Sep 2013.


New structures on DNA polymerases
-DNA pol B from P. abyssi by J. Gouge et al. (JMB)

New structures for ligand-gated ion channels
-A locally-closed form for GLIC here
-A review on cys-loop receptors here
-The paper on general anesthetics is here
-The structure of the open form is here


AquaSAXS, a web-based software to calculate SAXS spectra from PDB coordinates, including the solvent density predicted by AquaSol, is now available on-line. See article.
The corresponding software Aquasol to calculate solvation maps is also on line (see article).


A meeting in I. Pasteur of the France-Stanford Exchange Program (September)


MinActionPath was updated (NewPath) to accept up to 10,000 atoms thanks to Patrice Koehl (UC Davis, USA).


The dipolar solvent model was described in Biophysical Journal (coll. H. Orland).
The web server and new implementation due to P. Koehl (AquaSol) is here.


MinActionPath web server: Generate the most probable trajectory between two known structural forms of the same macromolecule (Franklin et al., 2007).


NOMAD-Ref web server
Normal Mode Analysis, Deformation and Refinement
PDB_Hydro web server
Mutation & Solvation: Dipolar Poisson-Boltzmannn


This site provides online servers for algorithms such as normal mode calculation, structural refinement, solvation, mutation and transition path calculation.
The primary application is for biological macromolecules like proteins or DNA or complexes thereof.

Go to Main site for more details on the group activities.

  Marc Delarue http://lorentz.dynstr.pasteur.fr