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Publications by year (2009-2019)


-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).

-A structural model for human Pol mu interacting with an NHEJ junction containing a DNA double-strand-break, based on crystal structures of a TdT chimera that recapitulates all properties of Pol mu, publsihed in JBC, see Access the
recommendation on F1000Prime. This is a collaboration with the group of M.R. Lieber (USA).

-Cryo-EM structure of the polD DNA polymerase (DP1+DP2) complex, with or without DNA, in PLoS Biol.

-An updated structure-based classification of all extant DNA polymerases (Here).

-An exploration of multidimensional representation of amino-acids to retrieve structural information from very large sequence alignments (Here). See also a recent Review in F1000.


-Molecular mechanism of proton gating in GLIC in PNAS and PDF.

-Fifth DNA Polymerases Meeting in Leiden, NL (Program here).

-CECAM Meeting on Normal Modes in IHP, Paris, September (Program here).

-New and faster calculations of Normal Modes with Patrice Koehl (Ref).

-Crystal structures of a new bacterial pentaLGIC at 2.3 Angstrom in a widely open form in PNAS and PDF.

-Positive and negative modulation of pentaLGICs by General Anesthetics in (Cell Rep. and F1000)

-Review on TdT in Current Opinion in Structural Biology (on line and F1000) and PDF.

-Design of a polymerase that generates libraries of random RNA in Nucleic Acids Res.


-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.)

-New methods in Normal Modes from Elastic Network Models (with Patrice Koehl) for automatic coarse-graining (JCTC) or dazzling speed (Front. Mol. Bios.)

-Organisation with Y.H. Sanejouand of a one day meeting in Normal Mode analysis and Conformational Transitions in Pasteur (30 May 2017)

-String method simulation of the transition pathway for GLIC, with Pr Toby W. Allen (Melbourne, Australia, corresp. author) in PNAS. See F1000

-X-ray structures of GLIC with Barbiturates, with Pr. Trevor Smart (UCL, UK) (J. Biol. Chem.) Editor's pick, Feb 3, 2017. See also here.


DNA Polymerases and DNA Repair

-X-ray structure of Archaeal polD DNA polymerase reveals a catalytic site similar to multi-subunit RNA polymerases that are found in all domains of life, by L. Sauguet, P. Raia, G. Henneke and M. Delarue (Nature Commun). See F1000.

-Structural basis for an unexpected "in trans" templated activity by TdT: implications for V(D)J recombination and DNA double-strand-breaks repair in eukaryotes, J. Loc'h, S. Rosario and M. Delarue (Structure). See F1000.

Pentameric Ligand-gated ion channels (pentaLGICs): drug binding sites in different conformational states

-X-ray structures of GLIC with Xenon, in the open and locally-closed states, with N. Colloc'h (PLoS One).
-X-ray structures of GLIC with Bromoform with MD studies by M. Baaden and coll. (Structure).


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

-Structure of a GLIC-GlyR chimera with P.-J. Corringer (PNAS, Feb 2015)
-Structural characterization of allosteric binding sites in GLIC (Acta D, March 2015) see F1000


-Structural basis for the gating mechanism in GLIC (PNAS, Jan 2014), see F1000
-A structural perspective in the pharmacology of pLGICs (BBA, May 2014)


-Structural basis for ion permeation in GLIC (EMBO Journal, Jan 2013) at 2.4 Angstrom
-Structural basis for alcohol potentiation in mutant of GLIC with R.J. Howard (Nature Comms, April 2013) see F1000

-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)
-Structures of inhibitors of Tdt, with G. Maga (Milan) and R. di Santo (Roma), J. Med. Chem., Sep 2013.


-Structure of Archaeal DNA polymerase (polB) from P. abyssi in editing mode by J. Gouge et al. (JMB)

-A review on cys-loop receptors with P.J. Corringer in Structure
-The locally-closed form for GLIC in 2012, see F1000


-The structure of a complex of general anesthetics with GLIC in 2011, see F1000


-1 micro-second long MD simulation of GLIC with Marc Baaden in 2010, see F1000


-The structure of the open form of GLIC with P.J. Corringer in 2009, see F1000

-The AquaSol model was extended to include solvent-solvent interactions in PRL, 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 dipolar solvent model was described in Biophysical Journal (coll. H. Orland).
The web server of AquaSol and a new implementation due to P. Koehl is here.

MinActionPath (MAP) web server can be used to generate the most probable trajectory between two known structural forms of the same macromolecule (Franklin et al., 2007).

Installation of NOMAD_Ref web server (see Ref. here).
Installation of PDB_Hydro web server (see Ref. here). This was later replaced by AquaSol.

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