Marc Delarue - Publications

Affiliations: 
Biologie Structural et Chimie Institut Pasteur, Paris, Paris, France 

64 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Koehl P, Delarue M, Orland H. Optimal transport at finite temperature. Physical Review. E. 100: 013310. PMID 31499816 DOI: 10.1103/PhysRevE.100.013310  1
2019 Koehl P, Delarue M, Orland H. Statistical Physics Approach to the Optimal Transport Problem. Physical Review Letters. 123: 040603. PMID 31491256 DOI: 10.1103/PhysRevLett.123.040603  1
2019 Loc'h J, Gerodimos CA, Rosario S, Tekpinar M, Lieber MR, Delarue M. Structural evidence for an base selection mechanism involving Loop1 in Polymerase mu at an NHEJ double-strand break junction. The Journal of Biological Chemistry. PMID 31138645 DOI: 10.1074/jbc.RA119.008739  1
2019 Raia P, Carroni M, Henry E, Pehau-Arnaudet G, Brûlé S, Béguin P, Henneke G, Lindahl E, Delarue M, Sauguet L. Structure of the DP1-DP2 PolD complex bound with DNA and its implications for the evolutionary history of DNA and RNA polymerases. Plos Biology. 17: e3000122. PMID 30657780 DOI: 10.1371/journal.pbio.3000122  1
2019 Raia P, Delarue M, Sauguet L. An updated structural classification of replicative DNA polymerases. Biochemical Society Transactions. PMID 30647142 DOI: 10.1042/BST20180579  1
2018 Koehl P, Orland H, Delarue M. Numerical Encodings of Amino Acids in Multivariate Gaussian Modeling of Protein Multiple Sequence Alignments. Molecules (Basel, Switzerland). 24. PMID 30597916 DOI: 10.3390/molecules24010104  1
2018 Hu H, Ataka K, Menny A, Fourati Z, Sauguet L, Corringer PJ, Koehl P, Heberle J, Delarue M. Electrostatics, proton sensor, and networks governing the gating transition in GLIC, a proton-gated pentameric ion channel. Proceedings of the National Academy of Sciences of the United States of America. PMID 30541892 DOI: 10.1073/pnas.1813378116  1
2018 Koehl P, Delarue M. Coarse-grained dynamics of supramolecules: Conformational changes in outer shells of Dengue viruses. Progress in Biophysics and Molecular Biology. PMID 30273615 DOI: 10.1016/j.pbiomolbio.2018.09.004  1
2018 Delarue M, Koehl P. Combined approaches from physics, statistics, and computer science for protein structure prediction: (unity is strength)? F1000research. 7. PMID 30079234 DOI: 10.12688/f1000research.14870.1  1
2018 Randrianjatovo-Gbalou I, Rosario S, Sismeiro O, Varet H, Legendre R, Coppée JY, Huteau V, Pochet S, Delarue M. Enzymatic synthesis of random sequences of RNA and RNA analogues by DNA polymerase theta mutants for the generation of aptamer libraries. Nucleic Acids Research. PMID 29788485 DOI: 10.1093/nar/gky413  1
2018 Fourati Z, Howard RJ, Heusser SA, Hu H, Ruza RR, Sauguet L, Lindahl E, Delarue M. Structural Basis for a Bimodal Allosteric Mechanism of General Anesthetic Modulation in Pentameric Ligand-Gated Ion Channels. Cell Reports. 23: 993-1004. PMID 29694907 DOI: 10.1016/j.celrep.2018.03.108  1
2018 Hu H, Nemecz Á, Van Renterghem C, Fourati Z, Sauguet L, Corringer PJ, Delarue M. Crystal structures of a pentameric ion channel gated by alkaline pH show a widely open pore and identify a cavity for modulation. Proceedings of the National Academy of Sciences of the United States of America. PMID 29632192 DOI: 10.1073/pnas.1717700115  1
2017 Nemecz Á, Hu H, Fourati Z, Van Renterghem C, Delarue M, Corringer PJ. 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. Plos Biology. 15: e2004470. PMID 29281623 DOI: 10.1371/journal.pbio.2004470  1
2017 Delarue M, Koehl P, Orland H. Ab initio sampling of transition paths by conditioned Langevin dynamics. The Journal of Chemical Physics. 147: 152703. PMID 29055326 DOI: 10.1063/1.4985651  1
2017 Lev B, Murail S, Poitevin F, Cromer BA, Baaden M, Delarue M, Allen TW. String method solution of the gating pathways for a pentameric ligand-gated ion channel. Proceedings of the National Academy of Sciences of the United States of America. PMID 28487483 DOI: 10.1073/pnas.1617567114  1
2017 Menny A, Lefebvre SN, Schmidpeter PA, Drège E, Fourati Z, Delarue M, Edelstein SJ, Nimigean CM, Joseph D, Corringer PJ. Identification of a pre-active conformation of a pentameric channel receptor. Elife. 6. PMID 28294942 DOI: 10.7554/eLife.23955  1
2017 Koehl P, Poitevin F, Navaza R, Delarue MH. The renormalization group and its applications to generating coarse-grained models of large biological molecular systems. Journal of Chemical Theory and Computation. PMID 28170254 DOI: 10.1021/acs.jctc.6b01136  1
2016 Hsieh YC, Poitevin F, Delarue M, Koehl P. Comparative Normal Mode Analysis of the Dynamics of DENV and ZIKV Capsids. Frontiers in Molecular Biosciences. 3: 85. PMID 28083537 DOI: 10.3389/fmolb.2016.00085  1
2016 Fourati Z, Ruza RR, Laverty D, Drège E, Delarue-Cochin S, Joseph D, Koehl P, Smart T, Delarue M. Barbiturates bind in the GLIC ion channel pore and cause inhibition by stabilizing a closed state. The Journal of Biological Chemistry. PMID 27986812 DOI: 10.1074/jbc.M116.766964  1
2016 Sauguet L, Raia P, Henneke G, Delarue M. Shared active site architecture between archaeal PolD and multi-subunit RNA polymerases revealed by X-ray crystallography. Nature Communications. 7: 12227. PMID 27548043 DOI: 10.1038/ncomms12227  1
2016 Loc'h J, Rosario S, Delarue M. Structural Basis for a New Templated Activity by Terminal Deoxynucleotidyl Transferase: Implications for V(D)J Recombination. Structure (London, England : 1993). PMID 27499438 DOI: 10.1016/j.str.2016.06.014  1
2016 Poitevin F, Delarue M, Orland H. Beyond Poisson-Boltzmann: Numerical Sampling of Charge Density Fluctuations. The Journal of Physical Chemistry. B. 120: 6270-7. PMID 27075231 DOI: 10.1021/acs.jpcb.6b02650  1
2016 Laurent B, Murail S, Shahsavar A, Sauguet L, Delarue M, Baaden M. Sites of Anesthetic Inhibitory Action on a Cationic Ligand-Gated Ion Channel. Structure (London, England : 1993). PMID 27021161 DOI: 10.1016/j.str.2016.02.014  1
2016 Sauguet L, Fourati Z, Prangé T, Delarue M, Colloc'h N. Structural Basis for Xenon Inhibition in a Cationic Pentameric Ligand-Gated Ion Channel. Plos One. 11: e0149795. PMID 26910105 DOI: 10.1371/journal.pone.0149795  1
2015 Gouge J, Rosario S, Romain F, Poitevin F, Béguin P, Delarue M. Structural basis for a novel mechanism of DNA bridging and alignment in eukaryotic DSB DNA repair. The Embo Journal. 34: 1126-42. PMID 25762590 DOI: 10.15252/embj.201489643  1
2015 Fourati Z, Sauguet L, Delarue M. Genuine open form of the pentameric ligand-gated ion channel GLIC. Acta Crystallographica. Section D, Biological Crystallography. 71: 454-60. PMID 25760595 DOI: 10.1107/S1399004714026698  1
2015 Moraga-Cid G, Sauguet L, Huon C, Malherbe L, Girard-Blanc C, Petres S, Murail S, Taly A, Baaden M, Delarue M, Corringer PJ. Allosteric and hyperekplexic mutant phenotypes investigated on an α1 glycine receptor transmembrane structure. Proceedings of the National Academy of Sciences of the United States of America. 112: 2865-70. PMID 25730860 DOI: 10.1073/pnas.1417864112  1
2015 Sauguet L, Shahsavar A, Delarue M. Crystallographic studies of pharmacological sites in pentameric ligand-gated ion channels. Biochimica Et Biophysica Acta. 1850: 511-23. PMID 24836522 DOI: 10.1016/j.bbagen.2014.05.007  1
2014 Weinreb V, Li L, Chandrasekaran SN, Koehl P, Delarue M, Carter CW. 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. The Journal of Biological Chemistry. 289: 4367-76. PMID 24394410 DOI: 10.1074/jbc.M113.538660  1
2014 Sauguet L, Shahsavar A, Poitevin F, Huon C, Menny A, Nemecz À, Haouz A, Changeux JP, Corringer PJ, Delarue M. Crystal structures of a pentameric ligand-gated ion channel provide a mechanism for activation. Proceedings of the National Academy of Sciences of the United States of America. 111: 966-71. PMID 24367074 DOI: 10.1073/pnas.1314997111  1
2013 Costi R, Crucitti GC, Pescatori L, Messore A, Scipione L, Tortorella S, Amoroso A, Crespan E, Campiglia P, Maresca B, Porta A, Granata I, Novellino E, Gouge J, Delarue M, et al. New nucleotide-competitive non-nucleoside inhibitors of terminal deoxynucleotidyl transferase: discovery, characterization, and crystal structure in complex with the target. Journal of Medicinal Chemistry. 56: 7431-41. PMID 23968551 DOI: 10.1021/jm4010187  1
2013 Gouge J, Rosario S, Romain F, Beguin P, Delarue M. Structures of intermediates along the catalytic cycle of terminal deoxynucleotidyltransferase: dynamical aspects of the two-metal ion mechanism. Journal of Molecular Biology. 425: 4334-52. PMID 23856622 DOI: 10.1016/j.jmb.2013.07.009  1
2013 Sauguet L, Howard RJ, Malherbe L, Lee US, Corringer PJ, Harris RA, Delarue M. Structural basis for potentiation by alcohols and anaesthetics in a ligand-gated ion channel. Nature Communications. 4: 1697. PMID 23591864 DOI: 10.1038/ncomms2682  1
2013 Smaoui MR, Poitevin F, Delarue M, Koehl P, Orland H, Waldispühl J. Computational assembly of polymorphic amyloid fibrils reveals stable aggregates. Biophysical Journal. 104: 683-93. PMID 23442919 DOI: 10.1016/j.bpj.2012.12.037  1
2013 Sauguet L, Poitevin F, Murail S, Van Renterghem C, Moraga-Cid G, Malherbe L, Thompson AW, Koehl P, Corringer PJ, Baaden M, Delarue M. Structural basis for ion permeation mechanism in pentameric ligand-gated ion channels. The Embo Journal. 32: 728-41. PMID 23403925 DOI: 10.1038/emboj.2013.17  1
2012 Giraut A, Abu El-Asrar R, Marlière P, Delarue M, Herdewijn P. 2'-Deoxyribonucleoside phosphoramidate triphosphate analogues as alternative substrates for E. coli polymerase III. Chembiochem : a European Journal of Chemical Biology. 13: 2439-44. PMID 23023962 DOI: 10.1002/cbic.201200413  1
2012 Gouge J, Ralec C, Henneke G, Delarue M. Molecular recognition of canonical and deaminated bases by P. abyssi family B DNA polymerase. Journal of Molecular Biology. 423: 315-36. PMID 22902479 DOI: 10.1016/j.jmb.2012.07.025  1
2012 Corringer PJ, Poitevin F, Prevost MS, Sauguet L, Delarue M, Changeux JP. Structure and pharmacology of pentameric receptor channels: from bacteria to brain. Structure (London, England : 1993). 20: 941-56. PMID 22681900 DOI: 10.1016/j.str.2012.05.003  1
2012 Prevost MS, Sauguet L, Nury H, Van Renterghem C, Huon C, Poitevin F, Baaden M, Delarue M, Corringer PJ. A locally closed conformation of a bacterial pentameric proton-gated ion channel. Nature Structural & Molecular Biology. 19: 642-9. PMID 22580559 DOI: 10.1038/nsmb.2307  1
2011 Nury H, Delarue M, Corringer PJ. [X-ray structures of general anesthetics bound to their molecular targets]. Medecine Sciences : M/S. 27: 1056-7. PMID 22192739 DOI: 10.1051/medsci/20112712006  1
2011 Koehl P, Orland H, Delarue M. Adapting Poisson-Boltzmann to the self-consistent mean field theory: application to protein side-chain modeling. The Journal of Chemical Physics. 135: 055104. PMID 21823735 DOI: 10.1063/1.3621831  1
2011 Poitevin F, Orland H, Doniach S, Koehl P, Delarue M. AquaSAXS: a web server for computation and fitting of SAXS profiles with non-uniformally hydrated atomic models. Nucleic Acids Research. 39: W184-9. PMID 21665925 DOI: 10.1093/nar/gkr430  1
2011 Nury H, Van Renterghem C, Weng Y, Tran A, Baaden M, Dufresne V, Changeux JP, Sonner JM, Delarue M, Corringer PJ. X-ray structures of general anaesthetics bound to a pentameric ligand-gated ion channel. Nature. 469: 428-31. PMID 21248852 DOI: 10.1038/nature09647  1
2010 Nury H, Poitevin F, Van Renterghem C, Changeux JP, Corringer PJ, Delarue M, Baaden M. One-microsecond molecular dynamics simulation of channel gating in a nicotinic receptor homologue. Proceedings of the National Academy of Sciences of the United States of America. 107: 6275-80. PMID 20308576 DOI: 10.1073/pnas.1001832107  1
2010 Koehl P, Delarue M. AQUASOL: An efficient solver for the dipolar Poisson-Boltzmann-Langevin equation. The Journal of Chemical Physics. 132: 064101. PMID 20151727 DOI: 10.1063/1.3298862  1
2010 Corringer PJ, Baaden M, Bocquet N, Delarue M, Dufresne V, Nury H, Prevost M, Van Renterghem C. Atomic structure and dynamics of pentameric ligand-gated ion channels: new insight from bacterial homologues. The Journal of Physiology. 588: 565-72. PMID 19995852 DOI: 10.1113/jphysiol.2009.183160  1
2010 Nury H, Bocquet N, Le Poupon C, Raynal B, Haouz A, Corringer PJ, Delarue M. Crystal structure of the extracellular domain of a bacterial ligand-gated ion channel. Journal of Molecular Biology. 395: 1114-27. PMID 19917292 DOI: 10.1016/j.jmb.2009.11.024  1
2009 Romain F, Barbosa I, Gouge J, Rougeon F, Delarue M. Conferring a template-dependent polymerase activity to terminal deoxynucleotidyltransferase by mutations in the Loop1 region. Nucleic Acids Research. 37: 4642-56. PMID 19502493 DOI: 10.1093/nar/gkp460  1
2009 Koehl P, Orland H, Delarue M. Computing ion solvation free energies using the dipolar Poisson model. The Journal of Physical Chemistry. B. 113: 5694-7. PMID 19385689 DOI: 10.1021/jp9010907  1
2009 Duclert-Savatier N, Poggi L, Miclet E, Lopes P, Ouazzani J, Chevalier N, Nilges M, Delarue M, Stoven V. Insights into the enzymatic mechanism of 6-phosphogluconolactonase from Trypanosoma brucei using structural data and molecular dynamics simulation. Journal of Molecular Biology. 388: 1009-21. PMID 19345229 DOI: 10.1016/j.jmb.2009.03.063  1
2009 Koehl P, Orland H, Delarue M. Beyond the Poisson-Boltzmann model: modeling biomolecule-water and water-water interactions. Physical Review Letters. 102: 087801. PMID 19257790 DOI: 10.1103/PhysRevLett.102.087801  1
2009 Laowanapiban P, Kapustina M, Vonrhein C, Delarue M, Koehl P, Carter CW. Independent saturation of three TrpRS subsites generates a partially assembled state similar to those observed in molecular simulations. Proceedings of the National Academy of Sciences of the United States of America. 106: 1790-5. PMID 19174517 DOI: 10.1073/pnas.0812752106  1
2009 Bocquet N, Nury H, Baaden M, Le Poupon C, Changeux JP, Delarue M, Corringer PJ. X-ray structure of a pentameric ligand-gated ion channel in an apparently open conformation. Nature. 457: 111-4. PMID 18987633 DOI: 10.1038/nature07462  1
2008 Azuara C, Orland H, Bon M, Koehl P, Delarue M. Incorporating dipolar solvents with variable density in Poisson-Boltzmann electrostatics. Biophysical Journal. 95: 5587-605. PMID 18820239 DOI: 10.1529/biophysj.108.131649  1
2007 Franklin J, Koehl P, Doniach S, Delarue M. MinActionPath: maximum likelihood trajectory for large-scale structural transitions in a coarse-grained locally harmonic energy landscape. Nucleic Acids Research. 35: W477-82. PMID 17545201 DOI: 10.1093/nar/gkm342  1
2007 Delarue M, Duclert-Savatier N, Miclet E, Haouz A, Giganti D, Ouazzani J, Lopez P, Nilges M, Stoven V. Three dimensional structure and implications for the catalytic mechanism of 6-phosphogluconolactonase from Trypanosoma brucei. Journal of Molecular Biology. 366: 868-81. PMID 17196981 DOI: 10.1016/j.jmb.2006.11.063  1
2006 Lindahl E, Azuara C, Koehl P, Delarue M. NOMAD-Ref: visualization, deformation and refinement of macromolecular structures based on all-atom normal mode analysis. Nucleic Acids Research. 34: W52-6. PMID 16845062 DOI: 10.1093/nar/gkl082  1
2006 Azuara C, Lindahl E, Koehl P, Orland H, Delarue M. PDB_Hydro: incorporating dipolar solvents with variable density in the Poisson-Boltzmann treatment of macromolecule electrostatics. Nucleic Acids Research. 34: W38-42. PMID 16845031 DOI: 10.1093/nar/gkl072  1
2006 Loth K, Abergel D, Pelupessy P, Delarue M, Lopes P, Ouazzani J, Duclert-Savatier N, Nilges M, Bodenhausen G, Stoven V. Determination of dihedral Psi angles in large proteins by combining NH(N)/C(alpha)H(alpha) dipole/dipole cross-correlation and chemical shifts. Proteins. 64: 931-9. PMID 16786593 DOI: 10.1002/prot.21063  1
2005 Lindahl E, Delarue M. Refinement of docked protein-ligand and protein-DNA structures using low frequency normal mode amplitude optimization. Nucleic Acids Research. 33: 4496-506. PMID 16087736 DOI: 10.1093/nar/gki730  1
2005 Taly A, Delarue M, Grutter T, Nilges M, Le Novère N, Corringer PJ, Changeux JP. Normal mode analysis suggests a quaternary twist model for the nicotinic receptor gating mechanism. Biophysical Journal. 88: 3954-65. PMID 15805177 DOI: 10.1529/biophysj.104.050229  1
2003 Haouz A, Vanheusden V, Munier-Lehmann H, Froeyen M, Herdewijn P, Van Calenbergh S, Delarue M. Enzymatic and structural analysis of inhibitors designed against Mycobacterium tuberculosis thymidylate kinase. New insights into the phosphoryl transfer mechanism. The Journal of Biological Chemistry. 278: 4963-71. PMID 12454011 DOI: 10.1074/jbc.M209630200  1
2002 Manallack DT, Pitt WR, Herdewijn P, Balzarini J, De Clercq E, Sanderson MR, Sohi M, Wien F, Munier-Lehmann H, Haouz A, Delarue M. Database searching for thymidine and thymidylate kinase inhibitors using three-dimensional structure-based methods. Journal of Enzyme Inhibition and Medicinal Chemistry. 17: 167-74. PMID 12443042 DOI: 10.1080/14756360290032949  1
2002 Ursby T, Weik M, Fioravanti E, Delarue M, Goeldner M, Bourgeois D. Cryophotolysis of caged compounds: a technique for trapping intermediate states in protein crystals. Acta Crystallographica. Section D, Biological Crystallography. 58: 607-14. PMID 11914484 DOI: 10.1107/S0907444902002135  1
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