Publications

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A
Abdollahi N, Albani A, Anthony E, Baud A, Cardon M, Clerc R, Czernecki D, Conte R, David L, Delaune A et al..  2018.  Meet-U: Educating through research immersion. PLOS Computational Biology. 14:1-10.
Abel S, Sterpone F, Bandyopadhyay S, Marchi M.  2004.  Molecular Modeling and Simulations of AOT−Water Reverse Micelles in Isooctane:  Structural and Dynamic Properties. J. Phys. Chem. B. 108:19458–19466.
Alharbi N, Alharbi M, Martinez X, Krone M, Rose AS, Baaden M, Laramee RS, Chavent M.  2017.  Molecular Visualization of Computational Biology Data: A Survey of Surveys. EuroVis 2017 - Short Papers.
B
Baaden M.  1999.  Molecular Modeling with the ChemOffice Ultra 4.5 program suite..
Baaden M, Schurhammer R, Wipff G.  2002.  Molecular dynamics study of the uranyl extraction by tri-n-butylphosphate (TBP): Demixing of water/''oil''/TBP solutions with a comparison of supercritical CO2 and chloroform. J. Phys. Chem. B. 106:434–441.
Baaden M, Meier C, Sansom MSP.  2003.  A molecular dynamics investigation of mono and dimeric states of the outer membrane enzyme OMPLA. J. Mol. Biol.. 331:177–189.
Baaden M, Berny F, Madic C, Wipff G.  2000.  M3+ lanthanide cation solvation by acetonitrile: The role of cation size, counterions, and polarization effects investigated by molecular dynamics and quantum mechanical simulations. J. Phys. Chem. A. 104:7659–7671.
Baaden M, Borthakur MPratim, Casanova S, Coalson R, Freger V, Gonzalez M, Góra A, Hinds B, Hirunpinyopas W, Hummer G et al..  2018.  The modelling and enhancement of water hydrodynamics: general discussion.. Faraday Discuss. 209:273-285.
Bastard J, Khac DDo, Fetizon M, Prévost C, Beloeil J-C.  1991.  Mechanism of the rearrangement of the bicyclo [4.2. 0] octan system to the bicyclo [3.2. 1] octan system. Tetrahedron. 47:229–238.
Beautrait A, Leroux V, Chavent M, Ghemtio L, Devignes M.-D, Smail-Tabbone M, Cai W, Shao X, Moreau G, Bladon P et al..  2008.  Multiple-step virtual screening using VSM-G: Overview and validation of fast geometrical matching enrichment. J. Mol. Model.. 14:393–401.
Beedle AEM, Lezamiz A, Stirnemann G, Garcia-Manyes S.  2015.  The mechanochemistry of copper reports on the directionality of unfolding in model cupredoxin proteins.. Nature Comm.. 6:7894.
Ben Ammar A, Soltanzadeh P, Bauché S, Richard P, Goillot E, Herbst R, Gaudon K, Huzé C, Schaeffer L, Yamanashi Y et al..  2013.  A mutation causes MuSK reduced sensitivity to agrin and congenital myasthenia. Plos One. 8
Bertucat G, Lavery R, Prévost C.  1998.  A model for parallel triple helix formation by RecA: single-single association with a homologous duplex via the minor groove. J. Biomol. Struct. Dyn.. 16:535–46.
Bertucat G, Lavery R, Prévost C.  2000.  A mechanism for RecA-promoted sequence homology recognition and strand exchange between single-stranded DNA and duplex DNA, via triple-helical intermediates. J. Biomol. Struct. Dyn.. :147–153.
Bertucat G, Lavery R, Prévost C.  1999.  A molecular model for RecA-promoted strand exchange via parallel triple-stranded helices. Biophys. J.. 77:1562–76.
Bestaoui-Berrekhchi-Berrahma N., Sekkal-Rahal M., Derreumaux P, Yousfi N..  2016.  MP2 and DFT studies of beta-D-neocarrabiose and beta-D-neocarrabiose monohydrate. Comput. Theor. Chem.. 1091:24–30.
Beveridge DL, Swaminathan S, Ravishanker G, Withka J, Srinivasan J, Prévost C, Louise-May S, DiCapua FM, Bolton PH.  1991.  Methodological considerations on molecular dynamics simulations of DNA oligonucleotides. AIP Conference Proceedings.
Bezukladnikov P.V, Elyakova L.A, Mazur AK.  1992.  Multiple attack in the mechanism of endoglucanase action. Bioorg. Chem.. 18:1141–1163.
Boyer B., Laurent B., Robert C.H, Prevost C..  2021.  Modeling Perturbations in Protein Filaments at the Micro and Meso Scale Using NAMD and PTools/Heligeom. Bio-protocol. 11:e4097.
Brandner AF, Timr S, Melchionna S, Derreumaux P, Baaden M, Sterpone F.  2019.  Modelling lipid systems in fluid with Lattice Boltzmann Molecular Dynamics simulations and hydrodynamics. Scientific Reports. 9:16450.
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.
C
Cazals F, Dreyfus T, Robert CH.  2013.  Modeling macromolecular complexes: a journey across scales. Modeling in Computational Biology and Biomedicine: A Multidisciplinary Endeavor.
Chavent M, Levy B, Maigret B.  2008.  MetaMol: High quality visualization of Molecular Skin Surface. J. Mol. Graphics Modell.. 27:209–213.
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.
Chiricotto M, Melchionna S, Derreumaux P, Sterpone F.  2019.  Multiscale Aggregation of the Amyloid Aβ16–22 Peptide: From Disordered Coagulation and Lateral Branching to Amorphous Prefibrils. The Journal of Physical Chemistry Letters. 10:1594-1599.

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