Publications

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2022
Bourassin N, Barbault F, Baaden M, Sacquin-Mora S.  2022.  Between Two Walls: Modeling the Adsorption Behavior of β-Glucosidase A on Bare and SAM-Functionalized Gold Surfaces.. Langmuir. 38(4):1313-1323.
Molza A-E, Westermaier Y, Moutte M, Ducrot P, Danilowicz C, Godoy-Carter V, Prentiss M, Robert CH, Baaden M, Prévost C.  2022.  Building Biological Relevance Into Integrative Modelling of Macromolecular Assemblies. Frontiers in Molecular Biosciences. 9:826136.
Puyo-Fourtine J, Juillé M, Hénin J, Clavaguéra C, Duboué-Dijon E.  2022.  Consistent Picture of Phosphate–Divalent Cation Binding from Models with Implicit and Explicit Electronic Polarization. J. Phys. Chem. B. 126(22):4022-4034.
Spalvieri D, Mauviel A-M, Lambert M, Ferey N, Sacquin-Mora S, Chavent M, Baaden M.  2022.  Design – a new way to look at old molecules. Journal of Integrative Bioinformatics. 19:20220020.
Hénin J, Lopes LJS, Fiorin G.  2022.  Human Learning for Molecular Simulations: The Collective Variables Dashboard in VMD.. J Chem Theory Comput. 18(3):1945-1956.
Karaca E, Prévost C, Sacquin-Mora S.  2022.  Modeling the Dynamics of Protein-Protein Interfaces, How and Why? Molecules. 27:1841.
Chávez-García C, Hénin J, Karttunen M.  2022.  Multiscale Computational Study of the Conformation of the Full-Length Intrinsically Disordered Protein MeCP2.. J Chem Inf Model. 62(4):958-970.
Petroff JT, Dietzen NM, Santiago-McRae E, Deng B, Washington MS, Chen LJ, K. Moreland T, Deng Z, Rau M, Fitzpatrick JAJ et al..  2022.  Open-channel structure of a pentameric ligand-gated ion channel reveals a mechanism of leaflet-specific phospholipid modulation. Nature Communications. 13
Ebrahimi M, Hénin J.  2022.  Symmetry-Adapted Restraints for Binding Free Energy Calculations.. J Chem Theory Comput.
O'Donnell T, Robert CH, Cazals F.  2022.  Tripeptide loop closure: A detailed study of reconstructions based on Ramachandran distributions. Proteins: Structure, Function, and Bioinformatics. 90:858-868.
2020
Nguyen PH, Sterpone F, Derreumaux P.  2020.  Aggregation of disease-related peptides.. Prog Mol Biol Transl Sci. 170:435-460.
de Oliveira DMendes, Zukowski SR, Palivec V, Hénin J, Martinez-Seara H, Ben-Amotz D, Jungwirth P, Duboué-Dijon E.  2020.  Binding of divalent cations to acetate: molecular simulations guided by Raman spectroscopy. Phys. Chem. Chem. Phys.. 22:24014-24027.
Migliore M, Bonvicini A, Tognetti V, Guilhaudis L, Baaden M, Oulyadi H, Joubert L, Ségalas-Milazzo I.  2020.  Characterization of β-turns by electronic circular dichroism spectroscopy: a coupled molecular dynamics and time-dependent density functional theory computational study.. Phys Chem Chem Phys. 22(3):1611-1623.
Baaden M.  2020.  Computer Simulations Provide Guidance for Molecular Medicine Through Insights on Dynamics and Mechanisms at the Atomic Scale. 7th International Conference on the Development of Biomedical Engineering in Vietnam (BME7).
Mazur AK, Nguyen T-S, Gladyshev E.  2020.  Direct Homologous dsDNA-dsDNA Pairing: How, Where, and Why? J Mol Biol. 432(3):737-744.
Ngo STung, Nguyen PH, Derreumaux P.  2020.  Impact of A2T and D23N Mutations on Tetrameric Aβ42 Barrel within a Dipalmitoylphosphatidylcholine Lipid Bilayer Membrane by Replica Exchange Molecular Dynamics.. J Phys Chem B. 124(7):1175-1182.
Hung HMinh, Nguyen MTho, Tran P-T, Truong VKhanh, Chapman J, Anh LHuu Quynh, Derreumaux P, Vu VV, Ngo STung.  2020.  Impact of the Astaxanthin, Betanin, and EGCG Compounds on Small Oligomers of Amyloid Aβ Peptide.. J Chem Inf Model. 60(3):1399-1408.
Bourassin N., Baaden M, Lojou E., Sacquin-Mora S.  2020.  Implicit Modeling of the Impact of Adsorption on Solid Surfaces for Protein Mechanics and Activity with a Coarse-Grained Representation. J Phys Chem B. 124:8516–8523.

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