Search Results - "Gready, Jill E."

Optimization of parameters for molecular dynamics simulation using smooth particle-mesh Ewald in GROMACS 4.5 by Abraham, Mark J., Gready, Jill E.

“…Based on our critique of requirements for performing an efficient molecular dynamics simulation with the particle‐mesh Ewald (PME) implementation in GROMACS…”
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The C‐type lectin‐like domain superfamily by Zelensky, Alex N, Gready, Jill E

“…The superfamily of proteins containing C‐type lectin‐like domains (CTLDs) is a large group of extracellular Metazoan proteins with diverse functions. The CTLD…”
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Combining docking and molecular dynamic simulations in drug design by Alonso, Hernán, Bliznyuk, Andrey A., Gready, Jill E.

“…A rational approach is needed to maximize the chances of finding new drugs, and to exploit the opportunities of potential new drug targets emerging from…”
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Directions for Optimization of Photosynthetic Carbon Fixation: RuBisCO's Efficiency May Not Be So Constrained After All by Cummins, Peter L, Kannappan, Babu, Gready, Jill E

“…The ubiquitous enzyme Ribulose 1,5-bisphosphate carboxylase-oxygenase (RuBisCO) fixes atmospheric carbon dioxide within the Calvin-Benson cycle that is…”
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Response: Commentary: Directions for Optimization of Photosynthetic Carbon Fixation: RuBisCO's Efficiency May Not Be So Constrained After All by Cummins, Peter L, Kannappan, Babu, Gready, Jill E

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Ensuring Mixing Efficiency of Replica-Exchange Molecular Dynamics Simulations by Abraham, Mark J, Gready, Jill E

“…We address the question of constructing a protocol for replica-exchange molecular dynamics (REMD) simulations that make efficient use of the replica space,…”
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Redefinition of Rubisco Carboxylase Reaction Reveals Origin of Water for Hydration and New Roles for Active-Site Residues by Kannappan, Babu, Gready, Jill E

“…Crystallographic, mutagenesis, kinetic, and computational studies on Rubisco over three decades have revealed much about its catalytic mechanism and the role…”
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Comparative analysis of structural properties of the C-type-lectin-like domain (CTLD) by Zelensky, Alex N., Gready, Jill E.

“…The superfamily of proteins containing the C‐type‐lectin‐like domain (CTLD) is a group of abundant extracellular metazoan proteins characterized by…”
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Kohn–Sham Density Functional Calculations Reveal Proton Wires in the Enolization and Carboxylase Reactions Catalyzed by Rubisco by Cummins, Peter L, Gready, Jill E

“…Ribulose 1,5-bisphosphate (RuBP) carboxylase-oxygenase (Rubisco) plays a fundamental role in the carbon cycle by fixing the atmospheric CO2 used in…”
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Revised mechanism of carboxylation of ribulose‐1,5‐biphosphate by rubisco from large scale quantum chemical calculations by Cummins, Peter L., Kannappan, Babu, Gready, Jill E.

“…Here, we describe a computational approach for studying enzymes that catalyze complex multi‐step reactions and apply it to Ribulose 1,5‐bisphosphate…”
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Ab Initio Molecular Dynamics Simulation and Energetics of the Ribulose-1,5-biphosphate Carboxylation Reaction Catalyzed by Rubisco: Toward Elucidating the Stereospecific Protonation Mechanism by Cummins, Peter L, Kannappan, Babu, Gready, Jill E

“…In the carboxylation reaction catalyzed by ribulose 1,5-bisphosphate (RuBP) carboxylase–oxygenase (Rubisco), which is fundamental to photosynthesis, scission…”
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Mechanism of Oxygenase-Pathway Reactions Catalyzed by Rubisco from Large-Scale Kohn–Sham Density Functional Calculations by Kannappan, Babu, Cummins, Peter L, Gready, Jill E

“…Ribulose 1,5-bisphosphate carboxylase-oxygenase (Rubisco) is the primary carbon-fixing enzyme in photosynthesis, fixing CO2 to a 5-carbon sugar, RuBP, in a…”
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Putative Functional Role for the Invariant Aspartate 263 Residue of Rhodospirillum rubrum Rubisco by Liggins, John R, Gready, Jill E

“…Although aspartate residue D263 of Rhodospirillum rubrum Rubisco is close to the active site and invariant in all reported Rubiscos, its possible functional…”
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C-type lectin-like domains in Fugu rubripes by Zelensky, Alex N, Gready, Jill E

“…Members of the C-type lectin domain (CTLD) superfamily are metazoan proteins functionally important in glycoprotein metabolism, mechanisms of multicellular…”
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Identification of Active-Site Residues of the Pro-Metastatic Endoglycosidase Heparanase by Hulett, Mark D, Hornby, June R, Ohms, Stephen J, Zuegg, Johannes, Freeman, Craig, Gready, Jill E, Parish, Christopher R

“…Heparanase is a β-d-endoglucuronidase that cleaves heparan sulfate (HS) and has been implicated in many important physiological and pathological processes,…”
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Conformation of Prion Protein Repeat Peptides Probed by FRET Measurements and Molecular Dynamics Simulations by Gustiananda, Marsia, Liggins, John R., Cummins, Peter L., Gready, Jill E.

“…We report the combined use of steady-state fluorescence resonance energy transfer (FRET) experiments and molecular dynamics (MD) simulations to investigate…”
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Copper-induced conformational change in a marsupial prion protein repeat peptide probed using FTIR spectroscopy by Gustiananda, Marsia, Haris, Parvez I., Milburn, Peter J., Gready, Jill E.

“…We report the first Fourier transform infrared analysis of prion protein (PrP) repeats and the first study of PrP repeats of marsupial origin. Large changes in…”
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Identification of the RGG Box Motif in Shadoo: RNA-Binding and Signaling Roles? by Corley, Susan M., Gready, Jill E.

“…Susan M. Corley and Jill E. Gready Computational Proteomics and Therapy Design Group, Division of Molecular Bioscience, John Curtin School of Medical Research,…”
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Integron-sequestered dihydrofolate reductase: a recently redeployed enzyme by Alonso, Hernán, Gready, Jill E.

“…The introduction and wide use of antibacterial drugs has resulted in the emergence of resistant organisms. DfrB dihydrofolate reductase (DHFR) is a bacterial…”
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Shadoo, a new protein highly conserved from fish to mammals and with similarity to prion protein by Premzl, Marko, Sangiorgio, Lorenzo, Strumbo, Bice, Marshall Graves, Jennifer A, Simonic, Tatjana, Gready, Jill E

“…We report evidence from cDNA isolation and expression analysis as well as analyses of genome, expressed sequence tag (EST), cDNA and expression databases for a…”
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