Publications

Export 809 results:
Author Title [ Type(Asc)] Year
Journal Article
Barboiu M, Kumar M, Baaden M, Gale PA, Hinds BJ.  2019.  Highlights from the Faraday Discussion on Artificial Water Channels, Glasgow, UK.. Chem Commun (Camb). 55(27):3853-3858.
Mazur AK.  1998.  Hierarchy of fast motions in protein dynamics. J. Phys. Chem. B. 102:473–479.
Robert CH.  1990.  A hierarchical `nesting' approach to describe the stability of alpha helices with side-chain interactions. Biopolymers. 30:335–347.
Lagarde N, Carbone A, Sacquin-Mora S.  2018.  Hidden partners: Using cross‐docking calculations to predict binding sites for proteins with multiple interactions. Proteins: Structure, Function, and Bioinformatics. 00:1-15.
Ziolkowska K, Derreumaux P, Folichon M, Pellegrini O, Regnier P, , Hajnsdorf E.  2006.  Hfq variant with altered RNA binding functions. Nucleic Acids Res.. 34:709–720.
Bocahut A., Derrien V., Bernad S., Sebban P., Sacquin-Mora S, Guittet E., Lescop E..  2013.  Heme orientation modulates histidine dissociation and ligand binding kinetics in the hexacoordinated human neuroglobin. J. Biol. Inorg. Chem.. 18:111–122.
Santini S, Derreumaux P.  2004.  Helix H1 of the prion protein is rather stable against environmental perturbations: molecular dynamics of mutation and deletion variants of PrP(90-231). Cell. Mol. Life Sci.. 61:951–960.
Qiu Y, Zhao Y, Becker M, John S, Parekh BS, Huang S, Hendarwanto A, Martinez ED, Chen Y, Lu H et al..  2006.  HDAC1 acetylation is linked to progressive modulation of steroid receptor-induced gene transcription.. Mol. Cell. 22:669–679.
Derreumaux P, VERGOTEN G.  1993.  HARMONIC AND MOLECULAR-DYNAMICS OF N-OCTANE - COMPARISON BETWEEN THE AMBER AND SPASIBA FORCE-FIELDS. J. Mol. Struct.. 295:233–244.
Mayer C., Timsit Y.  2001.  Hydration and structural alterations of A-DNA. Implications for the accuracy of DNA replication. Cell. Mol. Biol. (noisy-le-grand). 47:815–822.
Mayer-Jung C., Moras D., Timsit Y.  1998.  Hydration and recognition of methylated CpG steps in DNA. Embo J.. 17:2709–2718.
Gueroult M., Picot D., Abi-Ghanem J., Hartmann B., Baaden M.  2010.  How cations can assist DNase I in DNA binding and hydrolysis. Plos Comput. Biol.. 6:e1001000.
Vamparys L, Laurent B., Carbone A., Sacquin-Mora S.  2016.  Great interactions: How binding incorrect partners can teach us about protein recognition and function. Proteins: Struct., Funct., Bioinf.. :n/a-n/a.
Chavent M, Lévy B., Krone M., Bidmon K., Nominé J.P, Ertl T., Baaden M.  2011.  GPU-powered tools boost molecular visualization. Briefings Bioinf.. 12:689–701.
Chavent M, Vanel A., Tek A., Lévy B., Robert S., Raffin B., Baaden M.  2011.  GPU-accelerated atom and dynamic bond visualization using HyperBalls: a unified algorithm for balls, sticks and hyperboloids. J. Comput. Chem.. 32:2924–2935.
Jiang R., Lemoine D., Martz A., Taly A, Gonin S., L. de Carvalho P, Specht A., Grutter T..  2011.  Agonist trapped in ATP-binding sites of the P2X2 receptor. Proc. Natl. Acad. Sci. U.s.a.. 108:9066–9071.
Zaffagnini M, Marchand CH, Malferrari M, Murail S, Bonacchi S, Genovese D, Montalti M, Venturoli G, Falini G, Baaden M et al..  2019.  Glutathionylation primes soluble glyceraldehyde-3-phosphate dehydrogenase for late collapse into insoluble aggregates.. Proc Natl Acad Sci U S A. 116(51):26057-26065.
Petuhov M.G, Dorofeyev V.E, Abagyan R.A, Mazur AK.  1992.  Global optimization of conformation energy of polypeptides by tunnel algorithm. Biophysics. 37:226–230.
Prévost C, Takahashi M..  2003.  Geometry of the DNA strands within the RecA nucleofilament: role in homologous recombination. Q. Rev. Biophys.. 36:429–53.
Derreumaux P.  2000.  Generating ensemble averages for small proteins from extended conformations by Monte Carlo simulations. Phys. Rev. Lett.. 85:206–209.
Gresh N, Derreumaux P.  2003.  Generating conformations for two zinc-binding sites of HIV-1 nucleocapsid protein from random conformations by a hierarchical procedure and polarizable force field. J. Phys. Chem. B. 107:4862–4870.
LeBard DN, Hénin J, Eckenhoff RG, Klein ML, Brannigan G.  2012.  General Anesthetics Predicted to Block the GLIC Pore with Micromolar Affinity. Plos Comput. Biol.. 8:e1002532.
Calimet N., Simoes M., Changeux J.P, Karplus M., Taly A, Cecchini M..  2013.  A gating mechanism of pentameric ligand-gated ion channels. Proc. Natl. Acad. Sci. U.s.a.. 110:E3987–3996.
Bishop G.A, Parody-Morreale A., Robert C., Gill S.J and.  1987.  Gas-solution microcalorimeter for determining heat binding curves. Rev. Sci. Instr.. 58:632–638.
Timsit Y, Moras D..  1991.  Groove-backbone interaction in B-DNA. Implication for DNA condensation and recombination. J. Mol. Biol.. 221:919–940.

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