Publications

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2017
Katava M, Stirnemann G, Zanatta M, Capaccioli S, Pachetti M, Ngai KL, Sterpone F, Paciaroni A.  2017.  Critical structural fluctuations of proteins upon thermal unfolding challenge the Lindemann criterion. Proc Natl Acad Sci U S A. 114:9361-9366.
Katava M, Stirnemann G, Zanatta M, Capaccioli S, Pachetti M, Ngai KL, Sterpone F, Paciaroni A.  2017.  Critical structural fluctuations of proteins upon thermal unfolding challenge the Lindemann criterion. Proc Natl Acad Sci U S A. 114:9361-9366.
Colloc'h N., Sacquin-Mora S, Avella G., Dhaussy A.C, Prange T., Vallone B., Girard E..  2017.  Determinants of neuroglobin plasticity highlighted by joint coarse-grained simulations and high pressure crystallography. Sci Rep. 7:1858.
da Silva FLuis Barro, Derreumaux P, Pasquali S.  2017.  Fast coarse-grained model for RNA titration.. J Chem Phys. 146(3):035101.
Laurin Y, Eyer J, Robert CH, Prévost C, Sacquin-Mora S.  2017.  Mobility and core-protein binding patterns of disordered C-terminal tails in β-tubulin isotypes.. Biochemistry. 56(12):1746–1756.
Cragnolini T, Chakraborty D, Sponer J, Derreumaux P, Pasquali S, Wales DJ.  2017.  Multifunctional energy landscape for a DNA G-quadruplex: An evolved molecular switch.. J Chem Phys. 147(15):152715.
da Silva FLuis Barro, Derreumaux P, Pasquali S.  2017.  Protein-RNA complexation driven by the charge regulation mechanism.. Biochem Biophys Res Commun.
Lev B, Murail S, Poitevin F, Cromer BA, Baaden M, Delarue M, Allen TW.  2017.  String method solution of the gating pathways for a pentameric ligand-gated ion channel.. Proc Natl Acad Sci U S A. 114(21):E4158-E4167.
Kozlikova B., Krone M., Falk M., Lindow N., Baaden M, Baum D., Viola I., Parulek J., Hege H.-C..  2017.  Visualization of Biomolecular Structures: State of the Art Revisited: Visualization of Biomolecular Structures. Computer Graphics Forum. 36:178–204.
Mazzanti L, Doutreligne S, Gageat C, Derreumaux P, Taly A, Baaden M, Pasquali S.  2017.  What Can Human-Guided Simulations Bring to RNA Folding? Biophys J. 113(2):302-312.
2016
Stadlbauer P, Mazzanti L, Cragnolini T, Wales DJ, Derreumaux P, Pasquali S, Sponer J.  2016.  Coarse-Grained Simulations Complemented by Atomistic Molecular Dynamics Provide New Insights into Folding and Unfolding of Human Telomeric G-Quadruplexes. J. Chem. Theory Comput.. 12:6077–6097.
Nguyen PHoang, Sterpone F, Pouplana R, Derreumaux P, Campanera JM.  2016.  Dimerization Mechanism of Alzheimer A beta(40) Peptides: The High Content of Intrapeptide-Stabilized Conformations in A2V and A2T Heterozygous Dimers Retards Amyloid Fibril Formation. J. Phys. Chem. B. 120:12111–12126.
da Silva FLuis Barro, Pasquali S, Derreumaux P, Dias LGustavo.  2016.  Electrostatics analysis of the mutational and pH effects of the N-terminal domain self-association of the major ampullate spidroin. Soft Matter. 12:5600–5612.
Woll KA, Murlidaran S, Pinch BJ, Hénin J, Wang X, Salari R, Covarrubias M, Dailey WP, Brannigan G, Garcia BA et al..  2016.  A Novel Bifunctional Alkylphenol Anesthetic Allows Characterization of gamma-Aminobutyric Acid, Type A (GABAA), Receptor Subunit Binding Selectivity in Synaptosomes.. J. Biol. Chem. 291:20473–86.
Tran L, Basdevant N, Prévost C, Ha-Duong T.  2016.  Structure of ring-shaped Aβ42 oligomers determined by conformational selection. Sci. Rep.. 6:21429.
Katava M., Maccarini M., Villain G., Paciaroni A., Sztucki M., Ivanova O., Madern D., Sterpone F.  2016.  Thermal activation of ‘allosteric-like’ large-scale motions in a eukaryotic Lactate Dehydrogenase.. Sci. Reports. 7:41092.
Krone M., Kozlikova B., Lindow N., Baaden M, Baum D., Parulek J., Hege H.-C., Viola I..  2016.  Visual Analysis of Biomolecular Cavities: State of the Art. Comput. Graphics Forum. 35:527–551.
Kozlikova B., Krone M., Falk M., Lindow N., Baaden M, Baum D., Viola I., Parulek J., Hege H.-C..  2016.  Visualization of Biomolecular Structures: State of the Art Revisited. Comput. Graphics Forum.
Bellissent-Funel M-C., Hassanali A., Havenith M., Henchman R., Pohl P., Sterpone F, van der Spoel D., Xu Y., Garcia A.E.  2016.  Water Determines the Structure and Dynamics of Proteins. Chem. Rev.. 116:7673–7697.
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.
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.
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.
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.
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.

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