Publications

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Stirnemann G, Duboué-Dijon E, Laage D.  2017.  Ab Initio Simulations of Water Dynamics in Aqueous TMAO Solutions: Temperature and Concentration Effects. J Phys Chem B.
Bastard K, Saladin A, Prévost C.  2011.  Accounting for large amplitude protein deformation during in silico macromolecular docking. Int. J. Mol. Sci.. 12:1316–33.
Nguyen PH, Sterpone F, Derreumaux P.  2020.  Aggregation of disease-related peptides.. Prog Mol Biol Transl Sci. 170:435-460.
Mazur AK, Shepelyansky DL.  2015.  Algebraic Statistics of Poincaré Recurrences in a DNA Molecule.. Phys. Rev. Lett.. 115:188104.
Zhu S, Stroebel D, C Yao A, Taly A, Paoletti P.  2013.  Allosteric signaling and dynamics of the clamshell-like NMDA receptor GluN1 N-terminal domain. Nature Structural \& Molecular Biology. 20:477–485.
Nasica-Labouze J, Nguyen PH, Sterpone F, Berthoumieu O, Buchete N-V, Cote S, De Simone A, Doig AJ, Faller P, Garcia A et al..  2015.  Amyloid beta Protein and Alzheimer’s Disease: When Computer Simulations Complement Experimental Studies. Chem. Rev.. 115:3518–3563.
Nasica-Labouze J, Nguyen PH, Sterpone F, Berthoumieu O, Buchete N-V, Cote S, De Simone A, Doig AJ, Faller P, Garcia A et al..  2015.  Amyloid beta Protein and Alzheimer’s Disease: When Computer Simulations Complement Experimental Studies. Chem. Rev.. 115:3518–3563.
Lu Y, Shi X-F, Nguyen PH, Sterpone F, Jr FRSalsbury, Derreumaux P.  2019.  Amyloid-β (29–42) Dimeric Conformations in Membranes Rich in Omega-3 and Omega-6 Polyunsaturated Fatty Acids. The Journal of Physical Chemistry B. 123:2687–2696.
Lu Y, Shi X-F, Nguyen PH, Sterpone F, Jr FRSalsbury, Derreumaux P.  2019.  Amyloid-β (29–42) Dimeric Conformations in Membranes Rich in Omega-3 and Omega-6 Polyunsaturated Fatty Acids. The Journal of Physical Chemistry B. 123:2687–2696.
Gan H.H, Perow R.A, Roy S., , Yan S., Nicoletta A., D. Vafai SJ, Wang L., Noah J.E, Pasquali S. et al..  2002.  Analysis of Protein Sequence/Structure Similarity Relationships. Biophys. J.. 83:2781–2791.
Esque J, Sansom MSP, Baaden M, Oguey C.  2018.  Analyzing protein topology based on Laguerre tessellation of a pore-traversing water network.. Sci Rep. 8(1):13540.
Baaden M, Barboiu M, Borthakur MPratim, Chen C-L, Coalson R, Davis J, Freger V, Gong B, Hélix-Nielsen C, Hickey R et al..  2018.  Applications to water transport systems: general discussion.. Faraday Discuss. 209:389-414.
Baaden M, Barboiu M, Borthakur MPratim, Chen C-L, Coalson R, Davis J, Freger V, Gong B, Hélix-Nielsen C, Hickey R et al..  2018.  Applications to water transport systems: general discussion.. Faraday Discuss. 209:389-414.
Kalimeri M, Derreumaux P, Sterpone F.  2015.  Are coarse-grained models apt to detect protein thermal stability? The case of \OPEP\ force field J. Non-cryst. Solids. 407:494–501.
Chintapalli SV, Illingworth CJR, Upton GJG, Sacquin-Mora S, Reeves PJ, Mohammedali HS, Reynolds CA.  2014.  Assessing the effect of dynamics on the closed-loop protein-folding hypothesis. Journal of the Royal Society Interface. 11:20130935.
Krieger E., Leger L., Durrieu M.P., Taib N., Bond P., Laguerre M., Lavery R., Sansom M.S.P., Baaden M.  2007.  Atomistic modeling of the membrane-embedded synaptic fusion complex: a grand challenge project on the DEISA HPC infrastructure. ParCo 2007, Parallel Computing: Architectures, Algorithms and Applications. 38:729–736.
Schneider S., Saladin A, Fiorucci S., Prévost C, Zacharias M..  2012.  ATTRACT and PTOOLS: Open source programs for protein-protein docking. Methods Mol. Biol.. 819:221–232.
Schneider S., Saladin A, Fiorucci S., Prévost C, Zacharias M..  2012.  ATTRACT and PTOOLS: Open source programs for protein-protein docking. Methods Mol. Biol.. 819:221–232.

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