Publications

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2015
Cragnolini T, Derreumaux P, Pasquali S.  2015.  Ab initio RNA folding. Journal of Physics-condensed Matter. 27:233102.
Comer J, Gumbart JC, Hénin J, Lelièvre T, Pohorille A, Chipot C.  2015.  The adaptive biasing force method: everything you always wanted to know but were afraid to ask.. J. Phys. Chem. B. 119:1129–51.
Mazur AK, Shepelyansky DL.  2015.  Algebraic Statistics of Poincaré Recurrences in a DNA Molecule.. Phys. Rev. Lett.. 115:188104.
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.
Chakravarty D, Janin J, Robert CH, Chakrabarti P.  2015.  Changes in protein structure at the interface accompanying complex formation.. Iucrj. 2:643–652.
Cragnolini T, Laurin Y, Derreumaux P, Pasquali S.  2015.  Coarse-Grained HiRE-RNA Model for ab Initio RNA Folding beyond Simple Molecules, Including Noncanonical and Multiple Base Pairings. J. Chem. Theory Comput.. 11:3510–3522.
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.
Viet MHoang, Derreumaux P, Nguyen PHoang.  2015.  Communication: Multiple atomistic force fields in a single enhanced sampling simulation.. The Journal of Chemical Physics. 143:021101–021101.
Viet MHoang, Derreumaux P, Nguyen PHoang.  2015.  Communication: Multiple atomistic force fields in a single enhanced sampling simulation. J. Chem. Phys.. 143:021101.
Cazals F, Roth A, Dreyfus T, Mazauric D, Robert CH.  2015.  Conformational ensembles and sampled landscapes: analysis and comparison. J. Comp. Chem.. 36:1213–31.
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

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