Publications

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2010
Costa MGS, Batista PR, Shida CS, Robert CH, Bisch PM, Pascutti PG.  2010.  How does heparin prevent the pH inactivation of cathepsin B? Allosteric mechanism elucidated by docking and molecular dynamics. Bmc Genomics. 11, S5
Costa MGS, Batista PR, Shida CS, Robert CH, Bisch PM, Pascutti PG.  2010.  How does heparin prevent the pH inactivation of cathepsin B? Allosteric mechanism elucidated by docking and molecular dynamics. Bmc Genomics. 11, S5
Tek A, Laurent B, Férey N, Baaden M.  2010.  Interacting with Molecular Simulations using a Multimodal VR Framework. EuroVR-EVE. :1–4.
Saladin A, Amourda C., Poulain P., Férey N, Baaden M, Zacharias M, Delalande O., Prévost C.  2010.  Modeling the early stage of DNA sequence recognition within RecA nucleoprotein filaments. Nucleic Acids Res.. 38:6313–6323.
Delalande O., Férey N, Laurent B., Gueroult M., Hartmann B., Baaden M.  2010.  Multi-resolution approach for interactively locating functionally linked ion binding sites by steering small molecules into electrostatic potential maps using a haptic device. Pac. Symp. Biocomput.. :205–215.
Khalid S., Baaden M.  2010.  Molecular dynamics studies of outer membrane proteins : a story of barrels. :225–247.
Khalid S., Baaden M.  2010.  Molecular dynamics studies of outer membrane proteins : a story of barrels. :225–247.
Brannigan G, LeBard DN, Hénin J, Eckenhoff RG, Klein ML.  2010.  Multiple binding sites for the general anesthetic isoflurane identified in the nicotinic acetylcholine receptor transmembrane domain.. Proc. Natl. Acad. Sci. U.s.a.. 107:14122–14127.
Bedard-Hearn M., Sterpone F, Rossky P.J..  2010.  Non adiabatic simulations of exciton dissociation in poly-p-phenylenevinylene oligomers. J. Phys. Chem. A. 114:7661–7670.
Nury H., Poitevin F., Van Renterghem C., Changeux J.P, Corringer P.J, Delarue M., Baaden M.  2010.  One-microsecond molecular dynamics simulation of channel gating in a nicotinic receptor homologue. Proc. Natl. Acad. Sci. U.s.a.. 107:6275–6280.
Sinha D.K, Neveu P., Gagey N., Aujard I., Benbrahim-Bouzidi C., Le Saux T., Rampon C., Gauron C., Goetz B., Dubruille S. et al..  2010.  Photocontrol of protein activity in cultured cells and zebrafish with one- and two-photon illumination. Chembiochem. 11:653–663.
Sinha D.K, Neveu P., Gagey N., Aujard I., Benbrahim-Bouzidi C., Le Saux T., Rampon C., Gauron C., Goetz B., Dubruille S. et al..  2010.  Photocontrol of protein activity in cultured cells and zebrafish with one- and two-photon illumination. Chembiochem. 11:653–663.
Sinha D.K, Neveu P., Gagey N., Aujard I., Benbrahim-Bouzidi C., Le Saux T., Rampon C., Gauron C., Goetz B., Dubruille S. et al..  2010.  Photocontrol of protein activity in cultured cells and zebrafish with one- and two-photon illumination. Chembiochem. 11:653–663.
Chavent M, Vanel A., Lévy B., Raffin B., Tek A., Baaden M.  2010.  A Rendering Method for Small Molecules up to Macromolecular Systems: HyperBalls Accelerated by Graphics Processors. JOBIM.
Baaden M.  2010.  Simulations numériques de systèmes biologiques complexes : dynamique, structure et fonction de transporteurs, canaux et enzymes.
Hubert P, Sawma P, Duneau J-P, Khao J, Hénin J, Bagnard D, Sturgis J.  2010.  Single-spanning transmembrane domains in cell growth and cell-cell interactions: More than meets the eye? Cell Adh. Migr.. 4:313–324.
Zhang Y., Baaden M, Yan J., Shao J., Qiu S., Wu Y., Ding Y..  2010.  The molecular recognition mechanism for superoxide dismutase presequence binding to the mitochondrial protein import receptor Tom20 from Oryza sativa involves an LRTLA motif. J. Phys. Chem. B. 114:13839–13846.
Corringer P.J, Baaden M, Bocquet N., Delarue M., Dufresne V., Nury H., Prevost M., Van Renterghem C..  2010.  Atomic structure and dynamics of pentameric ligand-gated ion channels: new insight from bacterial homologues. J. Physiol. (lond.). 588:565–572.
Corringer P.J, Baaden M, Bocquet N., Delarue M., Dufresne V., Nury H., Prevost M., Van Renterghem C..  2010.  Atomic structure and dynamics of pentameric ligand-gated ion channels: new insight from bacterial homologues. J. Physiol. (lond.). 588:565–572.
Valleix S., Derreumaux P, Garnier C., Briki F., Boimard M., Doucet J., Rioux-Leclercq N., Martin L., Grateau G., Delpech M. et al..  2010.  The VLITL aggregation-prone motif might trigger amyloid fibril formation of fibrinogen A alpha-chain frameshift variants in vivo. Amyloid-journal of Protein Folding Disorders. 17:96–97.
Valleix S., Derreumaux P, Garnier C., Briki F., Boimard M., Doucet J., Rioux-Leclercq N., Martin L., Grateau G., Delpech M. et al..  2010.  The VLITL aggregation-prone motif might trigger amyloid fibril formation of fibrinogen A alpha-chain frameshift variants in vivo. Amyloid-journal of Protein Folding Disorders. 17:96–97.
Sterpone F, Bertonati C, Briganti G, Melchionna S.  2010.  Water around thermophilic proteins: the role of charged and apolar atoms. J Phys: Cond Matt. 22:284113.
Sterpone F, Bertonati C, Briganti G, Melchionna S.  2010.  Water around thermophilic proteins: the role of charged and apolar atoms. J Phys: Cond Matt. 22:284113.
2009
Durrieu M.P, Bond P.J, Sansom M.S, Lavery R., Baaden M.  2009.  Coarse-grain simulations of the R-SNARE fusion protein in its membrane environment detect long-lived conformational sub-states. Chemphyschem. 10:1548–1552.
Durrieu M.P, Bond P.J, Sansom M.S, Lavery R., Baaden M.  2009.  Coarse-grain simulations of the R-SNARE fusion protein in its membrane environment detect long-lived conformational sub-states. Chemphyschem. 10:1548–1552.

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