Publications
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Author Title Type [ Year
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2009. Energy Flow and Long-Range Correlations in Guanine-Binding Riboswitch: A Nonequilibrium Molecular Dynamics Study. J. Phys. Chem. B. 113:9340–9347.
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2009. Exploring amyloid aggregates with the OPEP coarse-grained force field. Abstracts of Papers of the American Chemical Society. 238
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2009. A fast method for large-scale De Novo peptide and miniprotein structure prediction.. J. Comput. Chem..
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2009. Induced beta-Barrel Formation of the Alzheimer’s A beta 25-35 Oligomers on Carbon Nanotube Surfaces: Implication for Amyloid Fibril Inhibition. Biophys. J.. 97:1795–1803.
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2009. Induced beta-barrel formation of the Alzheimer's Abeta25-35 oligomers on carbon nanotube surfaces: implication for amyloid fibril inhibition.. Biophys. J.. 97:1795–1803.
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2009. An optimized extended DNA kappa B site that enhances plasmid DNA nuclear import and gene expression. J. Gene Med.. 11:401–411.
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2009. New Insight into the interaction between erbin and smad3: a non-classical binding interface for the erbin PDZ domain. Biochem. Biophys. Res. Commun.. 378:360–365.
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2009. PEP-FOLD: an online resource for de novo peptide structure prediction. Nucleic Acids Res.. 37:W498-W503.
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2009. PEP-FOLD: an online resource for de novo peptide structure prediction.. Nucleic Acids Res.. 37:W498–W503.
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2009. Replica exchange molecular dynamics simulations of coarse-grained proteins in implicit solvent.. J. Phys. Chem. B. 113:267–274.
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2009. Replica exchange molecular dynamics simulations of coarse-grained proteins in implicit solvent.. J. Phys. Chem. B. 113:267–274.
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2009. Structural diversity of the soluble trimers of the human amylin(20-29) peptide revealed by molecular dynamics simulations. J. Chem. Phys.. 130:125101.
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2009. Structures and Thermodynamics of Alzheimer's Amyloid-beta A beta(16-35) Monomer and Dimer by Replica Exchange Molecular Dynamics Simulations: Implication for Full-Length A beta Fibrillation. J. Phys. Chem. B. 113:7668–7675.
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2009. Targeting the early steps of A beta 16-22 protofibril disassembly by N-methylated inhibitors: A numerical study. Proteins: Struct., Funct., Bioinf.. 75:442–452.
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2009. Thermodynamics and dynamics of amyloid peptide oligomerization are sequence dependent. Proteins: Struct., Funct., Bioinf.. 75:954–963.
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2009. X-ray structure of a pentameric ligand-gated ion channel in an apparently open conformation. Nature. 457:111–114.
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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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2010. Effects of the RGTFEGKF Inhibitor on the Structures of the Transmembrane Fragment 70-86 of Glycophorin A: An All-Atom Molecular Dynamics Study. J. Phys. Chem. B. 114:1004–1009.
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2010. A Fast Method for Large-Scale De Novo Peptide and Miniprotein Structure Prediction. J. Comput. Chem.. 31:726–738.
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2010. Functional Modes and Residue Flexibility Control the Anisotropic Response of Guanylate Kinase to Mechanical Stress. Biophys. J.. 99:3412–3419.
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2010. HiRE-RNA: A High Resolution Coarse-Grained Energy Model for RNA. J. Phys. Chem. B. 114:11957–11966.
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2010. Low molecular weight oligomers of amyloid peptides display beta-barrel conformations: A replica exchange molecular dynamics study in explicit solvent. J. Chem. Phys.. 132:165103.
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2010. Low molecular weight oligomers of amyloid peptides display beta-barrel conformations: A replica exchange molecular dynamics study in explicit solvent. J. Chem. Phys.. 132:165103.
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2010. Modeling the early stage of DNA sequence recognition within RecA nucleoprotein filaments. Nucleic Acids Res.. 38:6313–6323.