Publications
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2006. ARTIST: An activated method in internal coordinate space for sampling protein energy landscapes. Proteins: Struct., Funct., Bioinf.. 63:967–975.
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2011. Assessing the Quality of the OPEP Coarse-Grained Force Field. J. Chem. Theory Comput.. 7:1928–1934.
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2014. Atomic and Dynamic Insights into the Beneficial Effect of the 1,4-Naphthoquinon-2-yl-L-tryptophan Inhibitor on Alzheimer's A beta 1-42 Dimer in Terms of Aggregation and Toxicity. Acs Chem. Neurosci.. 5:148–159.
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2010. An atomistic model for simulations of the general anesthetic isoflurane. J. Phys. Chem. B. 114:604–612.
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2017. ATP hydrolysis provides functions that promote rejection of pairings between different copies of long repeated sequences. Nucleic Acids Res. 45:8448-8462.
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2005. The beta alpha beta alpha beta alpha elementary Supersecondary structure of the Rossmann fold from porcine lactate dehydrogenase exhibits characteristics of a molten globule. Proteins: Struct., Funct., Bioinf.. 60:740–745.
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2008. The beta-strand-loop-beta-strand conformation is marginally populated in beta(2)-microglobulin (20-41) peptide in solution as revealed by replica exchange molecular dynamics simulations. Biophys. J.. 95:510–517.
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2020. Binding of divalent cations to acetate: molecular simulations guided by Raman spectroscopy. Phys. Chem. Chem. Phys.. 22:24014-24027.
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2020. Binding of divalent cations to acetate: molecular simulations guided by Raman spectroscopy. Phys. Chem. Chem. Phys.. 22:24014-24027.
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2013. Biomolecular hydration dynamics: a jump model perspective. Chem. Soc. Rev.. 42:5672–5683.
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2018. Breaking down cellulose fibrils with a mid-infrared laser. Cellulose. 25:5553–5568.
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2018. Breaking down cellulose fibrils with a mid-infrared laser. Cellulose. 25:5553–5568.
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2022. Building Biological Relevance Into Integrative Modelling of Macromolecular Assemblies. Frontiers in Molecular Biosciences. 9:826136.
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2022. Building Biological Relevance Into Integrative Modelling of Macromolecular Assemblies. Frontiers in Molecular Biosciences. 9:826136.
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2021. Building intuition for binding free energy calculations: Bound state definition, restraints, and symmetry. The Journal of Chemical Physics. 154:204101.
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2009. Coarse-grain simulations of the R-SNARE fusion protein in its membrane environment detect long-lived conformational sub-states. Chemphyschem. 10:1548–1552.
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2008. Comparative models of P2X2 receptor support inter-subunit ATP-binding sites. Biochem. Biophys. Res. Commun.. 375:405–409.
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2009. Complex molecular assemblies at hand via interactive simulations. J. Comput. Chem.. 30:2375–2387.
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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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1987. Carbon dioxide and oxygen linkage in human hemoglobin tetramers. J. Mol. Biol.. 196:927–934.
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1987. Carbon dioxide and oxygen linkage in human hemoglobin tetramers. J. Mol. Biol.. 196:927–934.
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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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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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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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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.