Publications

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2015
Trellet M., Férey N, Baaden M, Bourdot P..  2015.  Content and task based navigation for structural biology in 3D environments. Virtual and Augmented Reality for Molecular Science (VARMS@IEEEVR), 2015 IEEE 1st International Workshop on. :31–36.
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
Zhang T, Nguyen PHoang, Nasica-Labouze J, Mu Y, Derreumaux P.  2015.  Folding Atomistic Proteins in Explicit Solvent Using Simulated Tempering. J. Phys. Chem. B. 119:6941–6951.
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.
Doig AJ, Derreumaux P.  2015.  Inhibition of protein aggregation and amyloid formation by small molecules. Curr. Opin. Struct. Biol.. 30:50–56.
Yang D, Boyer B, Prévost C, Danilowicz C, Prentiss M.  2015.  Integrating multi-scale data on homologous recombination into a new recognition mechanism based on simulations of the RecA-ssDNA/dsDNA structure. Nucleic Acids Res.. 43:10251–63.
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.
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
Tarus B, Nguyen PHoang, Berthoumieu O, Faller P, Doig AJ, Derreumaux P.  2015.  Molecular structure of the NQTrp inhibitor with the Alzheimer A beta 1-28 monomer. Eur. J. Med. Chem.. 91:43–50.
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.
Cragnolini T., Doutreligne S., Baaden M, Derreumaux P, Pasquali S..  2015.  Predicting and exploring complex nucleic acids architectures through a coarse-grained model. J. Biomol. Struct. Dyn.. 33 Suppl 1:30–31.
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.
Danilowicz C, Yang D, Kelley C, Prévost C, Prentiss M.  2015.  The poor homology stringency in the heteroduplex allows strand exchange to incorporate desirable mismatches without sacrificing recognition in vivo. Nucleic Acids Res.. 43:6473–85.
Cragnolini T., Doutreligne S., Baaden M, Derreumaux P, Pasquali S..  2015.  Predicting and exploring complex nucleic acids architectures through a coarse-grained model. Journal of Biomolecular Structure & Dynamics. 33:30–31.
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.
Nishikawa N, Nguyen PHoang, Derreumaux P, Okamoto Y.  2015.  Replica-exchange molecular dynamics simulation for understanding the initial process of amyloid peptide aggregation. Mol. Simul.. 41:1041–1044.
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.

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