Timeline

Marc Delarue

Head of Structure

01 Jul 2020

publication

Structural evidence for the binding of monocarboxylates and dicarboxylates at pharmacologically relevant extracellular sites of a pentameric ligand-gated ion channel.

16 Jun 2020

publication

Structural basis for allosteric transitions of a multidomain pentameric ligand-gated ion channel.

27 Mar 2020

publication

Structural basis for the increased processivity of D-family DNA polymerases in complex with PCNA.

26 Jul 2019

publication

Statistical Physics Approach to the Optimal Transport Problem.

28 May 2019

publication

Structural evidence for an “in trans” base selection mechanism involving Loop1 in polymerase μ at an NHEJ double-strand break junction

26 Mar 2019

publication

Rapid enzymatic synthesis of long RNA polymers: A simple protocol to generate RNA libraries with random sequences

13 Feb 2019

team

Structural Molecular Biology and Infectious Process

18 Jan 2019

publication

Structure of the DP1–DP2 PolD complex bound with DNA and its implications for the evolutionary history of DNA and RNA polymerases

18 Jan 2019

publication

Structure of the DP1-DP2 PolD complex bound with DNA and its implications for the evolutionary history of DNA and RNA polymerases

15 Jan 2019

publication

An updated structural classification of replicative DNA polymerases

28 Dec 2018

publication

Numerical Encodings of Amino Acids in Multivariate Gaussian Modeling of Protein Multiple Sequence Alignments

12 Dec 2018

publication

Electrostatics, proton sensor, and networks governing the gating transition in GLIC, a proton-gated pentameric ion channel

28 Sep 2018

publication

Coarse-grained dynamics of supramolecules: Conformational changes in outer shells of Dengue viruses

24 Jul 2018

publication

Combined approaches from physics, statistics, and computer science for protein structure prediction: (unity is strength)?

06 Jul 2018

publication

Enzymatic synthesis of random sequences of RNA and RNA analogues by DNA polymerase theta mutants for the generation of aptamer libraries

24 Apr 2018

publication

Structural Basis for a Bimodal Allosteric Mechanism of General Anesthetic Modulation in Pentameric Ligand-Gated Ion Channels

12 Apr 2018

publication

Terminal deoxynucleotidyltransferase: the story of an untemplated DNA polymerase capable of DNA bridging and templated synthesis across strands

09 Apr 2018

publication

Crystal structures of a pentameric ion channel gated by alkaline pH show a widely open pore and identify a cavity for modulation

15 Mar 2018

publication

Meet-U: Educating through research immersion

27 Dec 2017

publication

Full mutational mapping of titratable residues helps to identify proton-sensors involved in the control of channel gating in the Gloeobacter violaceus pentameric ligand-gated ion channel

21 Oct 2017

publication

Ab initio sampling of transition paths by conditioned Langevin dynamics

09 May 2017

publication

String method solution of the gating pathways for a pentameric ligand-gated ion channel

15 Mar 2017

publication

Identification of a pre-active conformation of a pentameric channel receptor

24 Feb 2017

publication

The Renormalization Group and Its Applications to Generating Coarse-Grained Models of Large Biological Molecular Systems

27 Dec 2016

publication

Comparative Normal Mode Analysis of the Dynamics of DENV and ZIKV Capsids

16 Dec 2016

publication

Barbiturates Bind in the GLIC Ion Channel Pore and Cause Inhibition by Stabilizing a Closed State

01 Oct 2016

publication

Vaccination Against Human Papilloma Viruses Leads to a Favorable Cytokine Profile of Specific T Cells

22 Aug 2016

publication

Shared active site architecture between archaeal PolD and multi-subunit RNA polymerases revealed by X-ray crystallography.

04 Aug 2016

publication

Structural Basis for a New Templated Activity by Terminal Deoxynucleotidyl Transferase: Implications for V(D)J Recombination

26 Apr 2016

publication

Beyond Poisson-Boltzmann: Numerical Sampling of Charge Density Fluctuations

24 Mar 2016

publication

Sites of Anesthetic Inhibitory Action on a Cationic Ligand-Gated Ion Channel

24 Feb 2016

publication

Structural Basis for Xenon Inhibition in a Cationic Pentameric Ligand-Gated Ion Channel

04 Aug 2015

software

AquaSol

30 Jul 2015

software

NOMAD-Ref

30 Jul 2015

project

DNA Repair and Cancer

08 Jul 2015

project

Ligand-gated Ion channels

11 May 2015

team

Structural Dynamics of Macromolecules

11 Mar 2015

publication

Structural basis for a novel mechanism of DNA bridging and alignment in eukaryotic DSB DNA repair

26 Feb 2015

publication

Genuine open form of the pentameric ligand-gated ion channel GLIC

17 Feb 2015

publication

Allosteric and hyperekplexic mutant phenotypes investigated on an α1 glycine receptor transmembrane structure

14 May 2014

publication

Crystallographic studies of pharmacological sites in pentameric ligand-gated ion channels

06 Jan 2014

publication

Enhanced amino acid selection in fully evolved tryptophanyl-tRNA synthetase, relative to its urzyme, requires domain motion sensed by the D1 switch, a remote dynamic packing motif

23 Dec 2013

publication

Crystal structures of a pentameric ligand-gated ion channel provide a mechanism for activation

12 Sep 2013

publication

New nucleotide-competitive non-nucleoside inhibitors of terminal deoxynucleotidyl transferase: discovery, characterization, and crystal structure in complex with the target

13 Jul 2013

publication

Structures of intermediates along the catalytic cycle of terminal deoxynucleotidyltransferase: dynamical aspects of the two-metal ion mechanism

12 Feb 2013

publication

Structural basis for ion permeation mechanism in pentameric ligand-gated ion channels

05 Feb 2013

publication

Computational assembly of polymorphic amyloid fibrils reveals stable aggregates

01 Jan 2013

publication

Structural basis for potentiation by alcohols and anaesthetics in a ligand-gated ion channel

28 Sep 2012

publication

2′-Deoxyribonucleoside phosphoramidate triphosphate analogues as alternative substrates for E. coli polymerase III

16 Aug 2012

publication

Molecular recognition of canonical and deaminated bases by P. abyssi family B DNA polymerase

06 Jun 2012

publication

Structure and pharmacology of pentameric receptor channels: from bacteria to brain

13 May 2012

publication

A locally closed conformation of a bacterial pentameric proton-gated ion channel

23 Dec 2011

publication

[X-ray structures of general anesthetics bound to their molecular targets]

07 Aug 2011

publication

Adapting Poisson-Boltzmann to the self-consistent mean field theory: application to protein side-chain modeling

10 Jun 2011

publication

AquaSAXS: a web server for computation and fitting of SAXS profiles with non-uniformally hydrated atomic models

20 Jan 2011

publication

X-ray structures of general anaesthetics bound to a pentameric ligand-gated ion channel

18 Aug 2010

publication

Structural insights into the quinolone resistance mechanism of Mycobacterium tuberculosis DNA gyrase

22 Mar 2010

publication

One-microsecond molecular dynamics simulation of channel gating in a nicotinic receptor homologue

14 Feb 2010

publication

AQUASOL: An efficient solver for the dipolar Poisson-Boltzmann-Langevin equation

07 Dec 2009

publication

Atomic structure and dynamics of pentameric ligand-gated ion channels: new insight from bacterial homologues

13 Nov 2009

publication

Crystal structure of the extracellular domain of a bacterial ligand-gated ion channel

05 Jun 2009

publication

Conferring a template-dependent polymerase activity to terminal deoxynucleotidyltransferase by mutations in the Loop1 region

30 Apr 2009

publication

Computing ion solvation free energies using the dipolar Poisson model

01 Apr 2009

publication

Insights into the enzymatic mechanism of 6-phosphogluconolactonase from Trypanosoma brucei using structural data and molecular dynamics simulation

24 Feb 2009

publication

Beyond the Poisson-Boltzmann model: modeling biomolecule-water and water-water interactions

27 Jan 2009

publication

Independent saturation of three TrpRS subsites generates a partially assembled state similar to those observed in molecular simulations

05 Nov 2008

publication

X-ray structure of a pentameric ligand-gated ion channel in an apparently open conformation

26 Sep 2008

publication

Incorporating dipolar solvents with variable density in Poisson-Boltzmann electrostatics

05 Dec 2007

publication

Dealing with structural variability in molecular replacement and crystallographic refinement through normal-mode analysis

01 Jun 2007

publication

MinActionPath: maximum likelihood trajectory for large-scale structural transitions in a coarse-grained locally harmonic energy landscape

12 Dec 2006

publication

An asymmetric underlying rule in the assignment of codons: possible clue to a quick early evolution of the genetic code via successive binary choices

22 Nov 2006

publication

Three dimensional structure and implications for the catalytic mechanism of 6-phosphogluconolactonase from Trypanosoma brucei

01 Sep 2006

publication

Determination of dihedral Psi angles in large proteins by combining NH(N)/C(alpha)H(alpha) dipole/dipole cross-correlation and chemical shifts

01 Jul 2006

publication

NOMAD-Ref: visualization, deformation and refinement of macromolecular structures based on all-atom normal mode analysis

01 Jul 2006

publication

PDB_Hydro: incorporating dipolar solvents with variable density in the Poisson-Boltzmann treatment of macromolecule electrostatics

08 Aug 2005

publication

Refinement of docked protein-ligand and protein-DNA structures using low frequency normal mode amplitude optimization

01 Apr 2005

publication

Normal mode analysis suggests a quaternary twist model for the nicotinic receptor gating mechanism

19 Apr 2004

publication

On the use of low-frequency normal modes to enforce collective movements in refining macromolecular structural models

25 Nov 2002

publication

Enzymatic and structural analysis of inhibitors designed against Mycobacterium tuberculosis thymidylate kinase. New insights into the phosphoryl transfer mechanism

01 Jun 2002

publication

Database searching for thymidine and thymidylate kinase inhibitors using three-dimensional structure-based methods

22 Mar 2002

publication

A little guide for advanced search:

Structural evidence for the binding of monocarboxylates and dicarboxylates at pharmacologically relevant extracellular sites of a pentameric ligand-gated ion channel.

Structural basis for allosteric transitions of a multidomain pentameric ligand-gated ion channel.

Structural basis for the increased processivity of D-family DNA polymerases in complex with PCNA.

Statistical Physics Approach to the Optimal Transport Problem.

Structural evidence for an “in trans” base selection mechanism involving Loop1 in polymerase μ at an NHEJ double-strand break junction

Rapid enzymatic synthesis of long RNA polymers: A simple protocol to generate RNA libraries with random sequences

Structural Molecular Biology and Infectious Process

Structure of the DP1–DP2 PolD complex bound with DNA and its implications for the evolutionary history of DNA and RNA polymerases

Structure of the DP1-DP2 PolD complex bound with DNA and its implications for the evolutionary history of DNA and RNA polymerases

An updated structural classification of replicative DNA polymerases

Numerical Encodings of Amino Acids in Multivariate Gaussian Modeling of Protein Multiple Sequence Alignments

Electrostatics, proton sensor, and networks governing the gating transition in GLIC, a proton-gated pentameric ion channel

Coarse-grained dynamics of supramolecules: Conformational changes in outer shells of Dengue viruses

Combined approaches from physics, statistics, and computer science for protein structure prediction: (unity is strength)?

Enzymatic synthesis of random sequences of RNA and RNA analogues by DNA polymerase theta mutants for the generation of aptamer libraries

Structural Basis for a Bimodal Allosteric Mechanism of General Anesthetic Modulation in Pentameric Ligand-Gated Ion Channels

Terminal deoxynucleotidyltransferase: the story of an untemplated DNA polymerase capable of DNA bridging and templated synthesis across strands

Crystal structures of a pentameric ion channel gated by alkaline pH show a widely open pore and identify a cavity for modulation

Meet-U: Educating through research immersion

Full mutational mapping of titratable residues helps to identify proton-sensors involved in the control of channel gating in the Gloeobacter violaceus pentameric ligand-gated ion channel

Ab initio sampling of transition paths by conditioned Langevin dynamics

String method solution of the gating pathways for a pentameric ligand-gated ion channel

Identification of a pre-active conformation of a pentameric channel receptor

The Renormalization Group and Its Applications to Generating Coarse-Grained Models of Large Biological Molecular Systems

Comparative Normal Mode Analysis of the Dynamics of DENV and ZIKV Capsids

Barbiturates Bind in the GLIC Ion Channel Pore and Cause Inhibition by Stabilizing a Closed State

Vaccination Against Human Papilloma Viruses Leads to a Favorable Cytokine Profile of Specific T Cells

Shared active site architecture between archaeal PolD and multi-subunit RNA polymerases revealed by X-ray crystallography.

Structural Basis for a New Templated Activity by Terminal Deoxynucleotidyl Transferase: Implications for V(D)J Recombination

Beyond Poisson-Boltzmann: Numerical Sampling of Charge Density Fluctuations

Sites of Anesthetic Inhibitory Action on a Cationic Ligand-Gated Ion Channel

Structural Basis for Xenon Inhibition in a Cationic Pentameric Ligand-Gated Ion Channel

AquaSol

NOMAD-Ref

DNA Repair and Cancer

Ligand-gated Ion channels

Structural Dynamics of Macromolecules

Structural basis for a novel mechanism of DNA bridging and alignment in eukaryotic DSB DNA repair

Genuine open form of the pentameric ligand-gated ion channel GLIC

Allosteric and hyperekplexic mutant phenotypes investigated on an α1 glycine receptor transmembrane structure

Crystallographic studies of pharmacological sites in pentameric ligand-gated ion channels

Enhanced amino acid selection in fully evolved tryptophanyl-tRNA synthetase, relative to its urzyme, requires domain motion sensed by the D1 switch, a remote dynamic packing motif

Crystal structures of a pentameric ligand-gated ion channel provide a mechanism for activation

New nucleotide-competitive non-nucleoside inhibitors of terminal deoxynucleotidyl transferase: discovery, characterization, and crystal structure in complex with the target

Structures of intermediates along the catalytic cycle of terminal deoxynucleotidyltransferase: dynamical aspects of the two-metal ion mechanism

Structural basis for ion permeation mechanism in pentameric ligand-gated ion channels

Computational assembly of polymorphic amyloid fibrils reveals stable aggregates

Structural basis for potentiation by alcohols and anaesthetics in a ligand-gated ion channel

2′-Deoxyribonucleoside phosphoramidate triphosphate analogues as alternative substrates for E. coli polymerase III

Molecular recognition of canonical and deaminated bases by P. abyssi family B DNA polymerase

Structure and pharmacology of pentameric receptor channels: from bacteria to brain

A locally closed conformation of a bacterial pentameric proton-gated ion channel

[X-ray structures of general anesthetics bound to their molecular targets]

Adapting Poisson-Boltzmann to the self-consistent mean field theory: application to protein side-chain modeling

AquaSAXS: a web server for computation and fitting of SAXS profiles with non-uniformally hydrated atomic models

X-ray structures of general anaesthetics bound to a pentameric ligand-gated ion channel

Structural insights into the quinolone resistance mechanism of Mycobacterium tuberculosis DNA gyrase

One-microsecond molecular dynamics simulation of channel gating in a nicotinic receptor homologue

AQUASOL: An efficient solver for the dipolar Poisson-Boltzmann-Langevin equation

Atomic structure and dynamics of pentameric ligand-gated ion channels: new insight from bacterial homologues

Crystal structure of the extracellular domain of a bacterial ligand-gated ion channel

Conferring a template-dependent polymerase activity to terminal deoxynucleotidyltransferase by mutations in the Loop1 region

Computing ion solvation free energies using the dipolar Poisson model

Insights into the enzymatic mechanism of 6-phosphogluconolactonase from Trypanosoma brucei using structural data and molecular dynamics simulation

Beyond the Poisson-Boltzmann model: modeling biomolecule-water and water-water interactions

Independent saturation of three TrpRS subsites generates a partially assembled state similar to those observed in molecular simulations

X-ray structure of a pentameric ligand-gated ion channel in an apparently open conformation

Incorporating dipolar solvents with variable density in Poisson-Boltzmann electrostatics

Dealing with structural variability in molecular replacement and crystallographic refinement through normal-mode analysis

MinActionPath: maximum likelihood trajectory for large-scale structural transitions in a coarse-grained locally harmonic energy landscape

An asymmetric underlying rule in the assignment of codons: possible clue to a quick early evolution of the genetic code via successive binary choices

Three dimensional structure and implications for the catalytic mechanism of 6-phosphogluconolactonase from Trypanosoma brucei

Determination of dihedral Psi angles in large proteins by combining NH(N)/C(alpha)H(alpha) dipole/dipole cross-correlation and chemical shifts

NOMAD-Ref: visualization, deformation and refinement of macromolecular structures based on all-atom normal mode analysis

PDB_Hydro: incorporating dipolar solvents with variable density in the Poisson-Boltzmann treatment of macromolecule electrostatics

Refinement of docked protein-ligand and protein-DNA structures using low frequency normal mode amplitude optimization

Normal mode analysis suggests a quaternary twist model for the nicotinic receptor gating mechanism

On the use of low-frequency normal modes to enforce collective movements in refining macromolecular structural models

Enzymatic and structural analysis of inhibitors designed against Mycobacterium tuberculosis thymidylate kinase. New insights into the phosphoryl transfer mechanism