Publications
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Author Title Type [ Year
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2013. coarse-grained models for protein folding ang aggregation. Methods Mol. Biol.. 924:585–600.
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2013. Coarse-Grained Simulations of RNA and DNA Duplexes. J. Phys. Chem. B. 117:8047–8060.
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2013. Communication: Simulated tempering with fast on-the-fly weight determination. J. Chem. Phys.. 138:061102.
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2013. Conformational Ensemble and Polymorphism of the All-Atom Alzheimer's A beta(37-42) Amyloid Peptide Oligomers. J. Phys. Chem. B. 117:5831–5840.
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2013. Density functional conformational study of 2-O-sulfated 3,6 anhydro-alpha-D-galactose and of neo-kappa- and iota-carrabiose molecules in gas phase and water. J. Mol. Model.. 19:893–904.
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2013. Effect of the Tottori Familial Disease Mutation (D7N) on the Monomers and Dimers of A beta(40) and A beta(42). Acs Chem. Neurosci.. 4:1446–1457.
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2013. Game on, science - how video game technology may help biologists tackle visualization challenges. Plos One. 8:e57990.
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2013. Heme orientation modulates histidine dissociation and ligand binding kinetics in the hexacoordinated human neuroglobin. J. Biol. Inorg. Chem.. 18:111–122.
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2013. Importance of the Ion-Pair Interactions in the OPEP Coarse-Grained Force Field: Parametrization and Validation. J. Chem. Theory Comput.. 9:4574–4584.
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2013. Interactive Molecular Dynamics: Scaling up to Large Systems.. Procedia Comput. Sci.. 18:20–29.
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2013. Modeling macromolecular complexes: a journey across scales. Modeling in Computational Biology and Biomedicine: A Multidisciplinary Endeavor.
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2013. Molecular Mechanism of the Inhibition of EGCG on the Alzheimer A beta(1-42) Dimer. J. Phys. Chem. B. 117:3993–4002.
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2013. Optical control of an ion channel gate. Proc. Natl. Acad. Sci. U.s.a.. 110:20813–20818.
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2013. Protein-protein interactions in a crowded environment: an analysis via cross-docking simulations and evolutionary information. Plos Comput. Biol.. 9:e1003369.
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2013. Replica-exchange molecular dynamics simulations of the amyloid-beta(16-22) fragments. European Biophysics Journal with Biophysics Letters. 42:S68.
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2013. Structural basis for ion permeation mechanism in pentameric ligand-gated ion channels. Embo J.. 32:728–741.
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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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2012. Configurational entropy: an improvement of the quasiharmonic approximation using configurational temperature. Phys. Chem. Chem. Phys.. 14:877–886.
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2012. Delivering the native structures of peptides from computer simulations and predicted NMR proton chemical shifts. J. Pept. Sci.. 18:S38.
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2012. Distinct Dimerization for Various Alloforms of the Amyloid-Beta Protein: A beta(1-40), A beta(1-42), and A beta(1-40)(D23N). J. Phys. Chem. B. 116:4043–4055.
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2012. Flexibility and binding affinity in protein-ligand, protein-protein and multi-component protein interactions: limitations of current computational approaches. Journal of the Royal Society Interface. 9:20–33.
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2012. Involvement of the cysteine-rich head domain in activation and desensitization of the P2X1 receptor. Proceedings of the National Academy of Sciences of the United States of America. 109:11396–11401.