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· NOMAD-Ref server
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· AquaSol server
· AquaSAXS server
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· New DSM web site
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· In the News

News (2006-2016)


DNA Polymerases and DNA Repair

-X-ray structure of Archaeal polD DNA polymerase reveals a catalytic site similar to multi-subunit RNA polymerases. L. Sauguet, P. Raia, G. Henneke and M. Delarue, Nature Comms. (Sept 2016)
This completes and provides a new paradigm for the classification of all extant DNA pols (F1000).

-Structural basis for a new templated activity by TdT: implications for V(D)J recombination,
by J. Loc'h, S. Rosario and M. Delarue, in Structure (Sep 2016).
Contrary to what was believed since its discovery, Tdt can copy DNA in a template-dependent mode, in trans. This informs us on the role of polX during NHEJ double-strand-break DNA Repair.

Pentameric Ligand-gated ion channels and general anesthetics

-X-ray structures of GLIC with Barbiturates, with Pr. Trevor Smart (UCL, UK), submitted.
-X-ray structures of GLIC with Xenon, in the open and pre-activation states (PLoS One).
-X-ray structures of GLIC with Bromoform with MD studies by M. Baaden and coll. (Structure).

-Recent Course in Crystallography on Phasing and Model Building in Paris (Here).
See also our papers on Methods in Crystallography (Methods).

New design for web server services: Try it!


Pentameric Ligand-gated ion channels

-pLGIC are Molecule of the Month in the PDB (Nov 2015)
-Structure of a GLIC-GlyR chimera (PNAS, Feb 2015)
-Structural characterization of allosteric acetate binding sites in GLIC (Acta D, March 2015) see F1000

DNA polymerases and DNA Repair

New TdT structures in complex with a DNA synapsis shed light on DNA Double-Strand-Break Repair by NHEJ (EMBO J., Mar 2015).


Ligand-gated ion channels

-Structural basis for the gating mechanism in GLIC (PNAS, Jan 2014), see F1000
See also Answers to some concerns about the true resolution of this structure
-A structural perspective in the pharmacology of pLGICs (BBA, May 2014)


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 Comms, April 2013) see F1000

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 review on cys-loop receptors here
-The locally-closed form for GLIC here, see F1000
-The paper on general anesthetics is here, see F1000
-The structure of the open form is here, see F1000



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.


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

A 1 micro-second long molecular dynamics simulation of GLIC is presented in PNAS, (see see F1000)


MinActionPath (MAP server) was updated (NewPath) to accept up to 10,000 atoms thanks to inew code by Patrice Koehl (UC Davis, USA).
A refinement on the dipolar solvent model has just been published in PRL, see F1000


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

An hypothesis on the rapid evolution of the genetic code based on the two classes of aminoacyl-tRNA synthetases: F1000


Installation of NOMAD_Ref and PDB_Hydro web servers (see Ref. here and here).
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
NOMAD-Ref web server
Normal Mode Refinement
PDB_Hydro web server
Mutation & Solvation: Dipolar solvent
PDB_Hydro web server
AquaSaxs web server

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