· Introduction/News

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

· References
· Homes & Links

· Recent papers

· Main site

· Google Scholar

News

2015

Ligand-gated ion channels

-Structure of a GLIC-GlyR chimera (PNAS, Feb 2015)
-Structural basis for acetate binding in GLIC (Acta Cryst D., March 2015)

DNA polymerases

Tdt new structures shed light on the microhomology base-pairing at a DNA synapsis during NHEJ and DNA Double-Strand-Break Repair (EMBO J., Mar 2015).

2014

Ligand-gated ion channels

-Structural basis for the gating mechanism in GLIC (PNAS, Jan 2014), see also Q & A
-A structural perspective in the pharmacology of pLGICs (BBA, May 2014)

2013

Ligand-gated ion channels

-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.

2012

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

2011

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). AquaSol replaces the old PDB_Hydro web server.

2010

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

2009

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

2008

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.

2007

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

2006

Installation of NOMAD_Ref and PDB_Hydro web servers.
These sites provide online servers for algorithms such as normal mode calculation, structural refinement, solvation, mutation and (later) 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.

NOMAD-Ref web server
Normal Mode Analysis
PDB_Hydro web server
Mutation & Solvation: Dipolar solvent
NOMAD-Ref web server
Normal Mode Refinement




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