Publications

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2015
Nasica-Labouze J, Nguyen PHoang, 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.
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.
Berthoumieu O, Nguyen PHoang, del Castillo-Frias MP, Ferre S, Tarus B, Nasica-Labouze J, Noel S, Saurel O, Rampon C, Doig AJ et al..  2015.  Combined Experimental and Simulation Studies Suggest a Revised Mode of Action of the Anti-Alzheimer Disease Drug NQ-Trp. Chemistry-a European Journal. 21:12657–12666.
Sacquin-Mora S, Prévost C.  2015.  Docking Peptides on Proteins: How to Open a Lock, in the Dark, with a Flexible Key. Structure. 23:1373–1374.
Laurent B, Chavent M, Cragnolini T, Dahl ACaroline E, Pasquali S, Derreumaux P, Sansom MSP, Baaden M.  2015.  Epock: rapid analysis of protein pocket dynamics. Bioinformatics. 31:1478–1480.
Valle-Orero J, Eckels E, Stirnemann G, Popa I, Berkovich R, Fernandez JM.  2015.  The elastic free energy of a tandem modular protein under force.. Biochem. Biophys. Res. Comm.. :1–5.
Sacquin-Mora S.  2015.  Fold and flexibility: what can proteins' mechanical properties tell us about their folding nucleus? J. R. Soc. Interface. 12
Mondal J, Halverson D, Li ITS, Stirnemann G, Walker GC, Berne BJ.  2015.  How osmolytes influence hydrophobic polymer conformations: A unified view from experiment and theory.. Proc. Natl. Acad. Sci. Usa. 112:9270–5.
Boyer B, Ezelin J, Poulain P, Saladin A, Zacharias M, Robert CH, Prévost C.  2015.  An integrative approach to the study of filamentous oligomeric assemblies, with application to RecA. Plos One. in press:e0116414.
Laurin Y., Savarin P., Robert CH, Takahashi M., Eyer J., Prévost C, Sacquin-Mora S.  2015.  Investigating the Structural Variability and Binding Modes of the Glioma Targeting NFL-TBS.40-63 Peptide on Tubulin. Biochemistry. 54:3660–3669.
Laurin Y., Savarin P., Robert CH, Takahashi M., Eyer J., Prévost C, Sacquin-Mora S.  2015.  Investigating the Structural Variability and Binding Modes of the Glioma Targeting NFL-TBS.40-63 Peptide on Tubulin. Biochemistry. 54:3660–3669.
Moraga-Cid G., Sauguet L., Huon C., Malherbe L., Girard-Blanc C., Petres S., Murail S., Taly A, Baaden M, Delarue M. et al..  2015.  Allosteric and hyperekplexic mutant phenotypes investigated on an α1 glycine receptor transmembrane structure. Proc. Natl. Acad. Sci. U.s.a.. 112:2865–2870.
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.
Cournia Z, Allen TW, Andricioaei I, Antonny B, Baum D, Brannigan G, Buchete N-V, Deckman JT, Delemotte L, Del Val C et al..  2015.  Membrane Protein Structure, Function, and Dynamics: a Perspective from Experiments and Theory.. J. Membr. Biol.. 248
Cournia Z, Allen TW, Andricioaei I, Antonny B, Baum D, Brannigan G, Buchete N-V, Deckman JT, Delemotte L, Del Val C et al..  2015.  Membrane Protein Structure, Function, and Dynamics: a Perspective from Experiments and Theory.. J. Membr. Biol.. 248
Reddy T., Shorthouse D., Parton D.L, Jefferys E., Fowler P.W, Chavent M, Baaden M, Sansom M.S.  2015.  Nothing to sneeze at: a dynamic and integrative computational model of an influenza A virion. Structure. 23:584–597.
Reddy T., Shorthouse D., Parton D.L, Jefferys E., Fowler P.W, Chavent M, Baaden M, Sansom M.S.  2015.  Nothing to sneeze at: a dynamic and integrative computational model of an influenza A virion. Structure. 23:584–597.
Viet MHoang, Derreumaux P, Li MSuan, Roland C, Sagui C, Nguyen PHoang.  2015.  Picosecond dissociation of amyloid fibrils with infrared laser: A nonequilibrium simulation study. J. Chem. Phys.. 143:155101.
Viet MHoang, Truong PMinh, Derreumaux P, Li MSuan, Roland C, Sagui C, Nguyen PHoang.  2015.  Picosecond melting of peptide nanotubes using an infrared laser: a nonequilibrium simulation study. Phys. Chem. Chem. Phys.. 17:27275–27280.
Sterpone F, Derreumaux P, Melchionna S.  2015.  Protein Simulations in Fluids: Coupling the OPEP Coarse-Grained Force Field with Hydrodynamics. J. Chem. Theory Comput.. 11:1843–1853.
Stirnemann G, Sterpone F.  2015.  Recovering protein thermal stability using all-atom Hamiltonian replica-exchange simulations in explicit solvent. J. Chem. Theo. Comput.. 11:5573–5577.
Stirnemann G, Sterpone F.  2015.  Recovering protein thermal stability using all-atom Hamiltonian replica-exchange simulations in explicit solvent. J. Chem. Theo. Comput.. 11:5573–5577.
Rahaman O, Kalimeri M, Melchionna S, Hénin J, Sterpone F.  2015.  Role of Internal Water on Protein Thermal Stability: The Case of Homologous G Domains.. J. Phys. Chem. B. 119:8939–49.
Chakraborty D, Taly A, Sterpone F.  2015.  Stay Wet, Stay Stable? How Internal Water Helps the Stability of Thermophilic Proteins The Journal of Physical Chemistry B. 119:12760–12770.
Tarus B, Tran T-T, Nasica-Labouze J, Sterpone F, Nguyen PHoang, Derreumaux P.  2015.  Structures of the Alzheimer’s Wild-Type A beta 1-40 Dimer from Atomistic Simulations. J. Phys. Chem. B. 119:10478–10487.

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