Publications
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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.
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2007. Coarse-grained protein molecular dynamics simulations. J. Chem. Phys.. 126:025101.
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2007. A coarse-grained protein force field for folding and structure prediction. Proteins: Struct., Funct., Bioinf.. 69:394–408.
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2012. The Coarse-Grained OPEP Force Field for Non-Amyloid and Amyloid Proteins. J. Phys. Chem. B. 116:8741–8752.
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2013. coarse-grained models for protein folding ang aggregation. Methods Mol. Biol.. 924:585–600.
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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.
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2016. Coarse-grained and All-atom Simulations towards the Early and Late Steps of Amyloid Fibril Formation. Isr. J. Chem.. DOI: 10.1002/ijch.201600048.
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2019. Coarse-grain simulations on NMR conformational ensembles highlight functional residues in proteins.. J R Soc Interface. 16(156):20190075.
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2005. Chromatin remodeling complexes: ATP-dependent machines in action.. Biochem. Cell Biol.. 83:405–417.
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2001. The chloroform TBP aqueous nitric acid interfacial system: a molecular dynamics investigation. J. Mol. Liq.. 90:1–9.
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2005. A chimera encoding the fusion of an acetylcholine-binding protein to an ion channel is stabilized in a state close to the desensitized form of ligand-gated ion channels. C. R. Biol.. 328:223–234.
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2014. CHARMM36 united atom chain model for lipids and surfactants.. J. Phys. Chem. B. 118:547–556.
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2020. Characterization of β-turns by electronic circular dichroism spectroscopy: a coupled molecular dynamics and time-dependent density functional theory computational study.. Phys Chem Chem Phys. 22(3):1611-1623.
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2024. The characterization of ancient Methanococcales malate dehydrogenases reveals that strong thermal stability prevents unfolding under intense γ-irradiation. Mol. Biol. Evol.. 41
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2011. On the characterization and selection of diverse conformational ensembles with applications to flexible docking. Ieee/acm Trans. Comput. Biol. Bioinform.. 8:487–98.
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2015. Changes in protein structure at the interface accompanying complex formation.. Iucrj. 2:643–652.
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2000. Cation coordination by calix[4]arenes bearing amide and/or phosphine oxide pendant groups: how many arms are needed to bind Li+ vs. Na+? A combined NMR and molecular dynamics study Journal of the Chemical Society-perkin Transactions 2. :1315–1321.
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1994. The catalytic mechanism of {$\alpha$}-amylases based upon enzyme crystal structures and model building calculations. Biochem. Biophys. Res. Commun.. 204:297–302.
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2011. Carbon Nanotube Inhibits the Formation of beta-Sheet-Rich Oligomers of the Alzheimer’s Amyloid-beta(16-22) Peptide. Biophys. J.. 101:2267–2276.
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1987. Carbon dioxide and oxygen linkage in human hemoglobin tetramers. J. Mol. Biol.. 196:927–934.
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1987. Calorimetric studies of oxygen and carbon monoxide binding to human hemoglobin. Sequential binding heats for oxygen. J. Biol. Chem.. 262:10994–10999.
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2000. Calix[4]arenes as selective extracting agents. An NMR dynamic and conformational investigation of the lanthanide(III) and thorium(IV) complexes. Inorg. Chem.. 39:2033–2041.
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1992. Crystallization of DNA. Meth. Enzymol.. 211:409–429.
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1996. Cruciform structures and functions. Q. Rev. Biophys.. 29:279–307.
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2001. Convergent evolution of MutS and topoisomerase II for clamping DNA crossovers and stacked Holliday junctions. J. Biomol. Struct. Dyn.. 19:215–218.