Publications

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Dorofeyev VE, Mazur AK.  1993.  Investigation of conformational equilibrium of polypeptides by internal coordinate stochastic dynamics: Met-enkephalin. J. Biomol. Struct. Dyn.. 10:143–167.
Dorofeyev VE, Mazur AK.  1993.  Optimization of numerical algorithms for internal coordinate molecular dynamics. J. Comput. Phys.. 107:359–366.
Doutreligne S., Gageat C., Cragnolini T., Taly A, Pasquali S., Derreumaux P, Baaden M.  2015.  UnityMol: interactive and ludic visual manipulation of coarse-grained RNA and other biomolecules. Virtual and Augmented Reality for Molecular Science (VARMS@IEEEVR), 2015 IEEE 1st International Workshop on. :1–6.
Doutreligne S., Cragnolini T., Pasquali S., Derreumaux P, Baaden M.  2014.  UnityMol: Interactive scientific visualization for integrative biology. Large Data Analysis and Visualization (LDAV), 2014 IEEE 4th Symposium on. :109–110.
Doyle ML, Di Cera E, Robert CH, Gill SJ.  1987.  Carbon dioxide and oxygen linkage in human hemoglobin tetramers. J. Mol. Biol.. 196:927–934.
Dragelj J, Karafoulidi-Retsou C, Katz S, Lenz O, Zebger I, Caserta G, Sacquin-Mora S, Mroginski MAndrea.  2023.  Conformational and mechanical stability of the isolated large subunit of membrane-bound [NiFe]-hydrogenase from Cupriavidus necator. Frontiers in Microbiology. 13
Dreher M., Piuzzi M., Turki A., Chavent M, Baaden M, Férey N, Limet S., Raffin B., Robert S..  2013.  Interactive Molecular Dynamics: Scaling up to Large Systems.. Procedia Comput. Sci.. 18:20–29.
Dreher M, Prevoteau-Jonquet J, Trellet M, Piuzzi M, Baaden M, Raffin B, Férey N, Robert S, Limet S..  2014.  ExaViz: a flexible framework to analyse, steer and interact with molecular dynamics simulations. Faraday Discuss.. 169:119–142.
Drevelle A, Urvoas A, Ben Hamida-Rebai M, Van Vooren G, Nicaise M, Valerio-Lepiniec M, Desmadril M, Robert CH, Minard P.  2009.  Disulfide bond substitution by directed evolution in an engineered binding-protein scaffold.. Chembiochem. 10:1349–1359.
Duboué-Dijon E, Hénin J.  2021.  Building intuition for binding free energy calculations: Bound state definition, restraints, and symmetry. The Journal of Chemical Physics. 154:204101.
Duboué-Dijon E, Javanainen M, Delcroix P, Jungwirth P, Martinez-Seara H.  2020.  A practical guide to biologically relevant molecular simulations with charge scaling for electronic polarization.. J Chem Phys. 153(5):050901.
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, Lavery R, Baaden M.  2008.  Interactions between neuronal fusion proteins explored by molecular dynamics. Biophys. J.. 94:3436–3446.

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