Publications
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2010. DNA structures from phosphate chemical shifts. Nucleic Acids Res.. 38:e18.
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2010. Direct evidence of angular jumps during water reorientation through two-dimensional infrared anisotropy. J. Phys. Chem. Lett.. 1:1511–1516.
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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. Exploring Multidimensional Free Energy Landscapes Using Time-Dependent Biases on Collective Variables. J. Chem. Theory Comput.. 6:35–47.
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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. How cations can assist DNase I in DNA binding and hydrolysis. Plos Comput. Biol.. 6:e1001000.
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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. How does heparin prevent the pH inactivation of cathepsin B? Allosteric mechanism elucidated by docking and molecular dynamics. Bmc Genomics. 11, S5
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2010. Intrinsic flexibility of B-DNA: the experimental TRX scale. Nucleic Acids Res.. 38:1034–1047.
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2010. Infrared signatures of the peptide dynamical transition: A molecular dynamics simulation study. J. Chem. Phys.. 133
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2010. Interacting with Molecular Simulations using a Multimodal VR Framework. EuroVR-EVE. :1–4.
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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.
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2010. Multi-resolution approach for interactively locating functionally linked ion binding sites by steering small molecules into electrostatic potential maps using a haptic device. Pac. Symp. Biocomput.. :205–215.
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2010. Molecular dynamics studies of outer membrane proteins : a story of barrels. :225–247.
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2010. Multiple binding sites for the general anesthetic isoflurane identified in the nicotinic acetylcholine receptor transmembrane domain.. Proc. Natl. Acad. Sci. U.s.a.. 107:14122–14127.
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2010. Non adiabatic simulations of exciton dissociation in poly-p-phenylenevinylene oligomers. J. Phys. Chem. A. 114:7661–7670.
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2010. Nonequilibrium molecular dynamics simulation of the energy transport through a peptide helix. J. Chem. Phys.. 132
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2010. One-microsecond molecular dynamics simulation of channel gating in a nicotinic receptor homologue. Proc. Natl. Acad. Sci. U.s.a.. 107:6275–6280.
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2010. Photocontrol of protein activity in cultured cells and zebrafish with one- and two-photon illumination. Chembiochem. 11:653–663.
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2010. Protein-Protein Docking. Protein-Protein Complexes. Analysis, Modeling and Drug Design. :147–181.
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2010. A putative extracellular salt bridge at the subunit interface contributes to the ion channel function of the ATP-gated P2X2 receptor. J. Biol. Chem.. 285:15805–15815.