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Optimization of parameters for molecular dynamics simulation using smooth particle-mesh Ewald in GROMACS 4.5

Journal of computational chemistry, 2011-07, Vol.32 (9), p.2031-2040

2011

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The C‐type lectin‐like domain superfamily

The FEBS journal, 2005-12, Vol.272 (24), p.6179-6217

2005

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Combining docking and molecular dynamic simulations in drug design

Medicinal research reviews, 2006-09, Vol.26 (5), p.531-568

2006

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Directions for Optimization of Photosynthetic Carbon Fixation: RuBisCO's Efficiency May Not Be So Constrained After All

Frontiers in plant science, 2018-03, Vol.9, p.183-183

2018

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Response: Commentary: Directions for Optimization of Photosynthetic Carbon Fixation: RuBisCO's Efficiency May Not Be So Constrained After All

Frontiers in plant science, 2019-11, Vol.10, p.1426-1426

2019

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Ensuring Mixing Efficiency of Replica-Exchange Molecular Dynamics Simulations

Journal of chemical theory and computation, 2008-07, Vol.4 (7), p.1119-1128

2008

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Redefinition of Rubisco Carboxylase Reaction Reveals Origin of Water for Hydration and New Roles for Active-Site Residues

Journal of the American Chemical Society, 2008-11, Vol.130 (45), p.15063-15080

2008

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Kohn–Sham Density Functional Calculations Reveal Proton Wires in the Enolization and Carboxylase Reactions Catalyzed by Rubisco

The journal of physical chemistry. B, 2020-04, Vol.124 (15), p.3015-3026

2020

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Revised mechanism of carboxylation of ribulose‐1,5‐biphosphate by rubisco from large scale quantum chemical calculations

Journal of computational chemistry, 2018-08, Vol.39 (21), p.1656-1665

2018

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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

The journal of physical chemistry. B, 2019-03, Vol.123 (12), p.2679-2686

2019

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Mechanism of Oxygenase-Pathway Reactions Catalyzed by Rubisco from Large-Scale Kohn–Sham Density Functional Calculations

The journal of physical chemistry. B, 2019-04, Vol.123 (13), p.2833-2843

2019

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C-type lectin-like domains in Fugu rubripes

BMC genomics, 2004-08, Vol.5 (1), p.51-51, Article 51

2004

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Identification of Active-Site Residues of the Pro-Metastatic Endoglycosidase Heparanase

Biochemistry (Easton), 2000-12, Vol.39 (51), p.15659-15667

2000

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Putative Functional Role for the Invariant Aspartate 263 Residue of Rhodospirillum rubrum Rubisco

Biochemistry (Easton), 2009-03, Vol.48 (10), p.2226-2236

2009

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Conformation of Prion Protein Repeat Peptides Probed by FRET Measurements and Molecular Dynamics Simulations

Biophysical journal, 2004-04, Vol.86 (4), p.2467-2483

2004

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Shadoo, a new protein highly conserved from fish to mammals and with similarity to prion protein

Gene, 2003-09, Vol.314, p.89-102

2003

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Integron-sequestered dihydrofolate reductase: a recently redeployed enzyme

Trends in microbiology (Regular ed.), 2006-05, Vol.14 (5), p.236-242

2006

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Synthesis of quaternised 2-aminopyrimido[4,5- d]pyrimidin-4(3 H)-ones and their biological activity with dihydrofolate reductase

European journal of medicinal chemistry, 2003-07, Vol.38 (7), p.719-728

2003

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Copper-induced conformational change in a marsupial prion protein repeat peptide probed using FTIR spectroscopy

FEBS letters, 2002-02, Vol.512 (1), p.38-42

2002

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Methyltetrahydrofolate:corrinoid/iron−sulfur Protein Methyltransferase (MeTr): Protonation State of the Ligand and Active-Site Residues

The journal of physical chemistry. B, 2009-11, Vol.113 (44), p.14787-14796

2009

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Molecular dynamics simulation of human prion protein including both N-linked oligosaccharides and the GPI anchor

Glycobiology (Oxford), 2000-10, Vol.10 (10), p.959-974

2000

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Evolution of vertebrate genes related to prion and Shadoo proteins--clues from comparative genomic analysis

Molecular biology and evolution, 2004-12, Vol.21 (12), p.2210-2231

2004

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Energetically Most Likely Substrate and Active-Site Protonation Sites and Pathways in the Catalytic Mechanism of Dihydrofolate Reductase

Journal of the American Chemical Society, 2001-04, Vol.123 (15), p.3418-3428

2001

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Calculation of a Complete Enzymic Reaction Surface: Reaction and Activation Free Energies for Hydride-Ion Transfer in Dihydrofolate Reductase

Journal of chemical theory and computation, 2007-05, Vol.3 (3), p.1203-1211

2007

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CO2 Fixation by Rubisco: Computational Dissection of the Key Steps of Carboxylation, Hydration, and C−C Bond Cleavage

Journal of the American Chemical Society, 2001-11, Vol.123 (44), p.10821-10829

2001

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Optimization of parameters for molecular dynamics simulation using smooth particle-mesh Ewald in GROMACS 4.5

The C‐type lectin‐like domain superfamily

Combining docking and molecular dynamic simulations in drug design

Directions for Optimization of Photosynthetic Carbon Fixation: RuBisCO's Efficiency May Not Be So Constrained After All

Response: Commentary: Directions for Optimization of Photosynthetic Carbon Fixation: RuBisCO's Efficiency May Not Be So Constrained After All

Ensuring Mixing Efficiency of Replica-Exchange Molecular Dynamics Simulations

Redefinition of Rubisco Carboxylase Reaction Reveals Origin of Water for Hydration and New Roles for Active-Site Residues

Kohn–Sham Density Functional Calculations Reveal Proton Wires in the Enolization and Carboxylase Reactions Catalyzed by Rubisco

Revised mechanism of carboxylation of ribulose‐1,5‐biphosphate by rubisco from large scale quantum chemical calculations

Ab Initio Molecular Dynamics Simulation and Energetics of the Ribulose-1,5-biphosphate Carboxylation Reaction Catalyzed by Rubisco: Toward Elucidating the Stereospecific Protonation Mechanism

Mechanism of Oxygenase-Pathway Reactions Catalyzed by Rubisco from Large-Scale Kohn–Sham Density Functional Calculations

C-type lectin-like domains in Fugu rubripes

Identification of Active-Site Residues of the Pro-Metastatic Endoglycosidase Heparanase

Putative Functional Role for the Invariant Aspartate 263 Residue of Rhodospirillum rubrum Rubisco

Conformation of Prion Protein Repeat Peptides Probed by FRET Measurements and Molecular Dynamics Simulations

Shadoo, a new protein highly conserved from fish to mammals and with similarity to prion protein

Integron-sequestered dihydrofolate reductase: a recently redeployed enzyme

Synthesis of quaternised 2-aminopyrimido[4,5- d]pyrimidin-4(3 H)-ones and their biological activity with dihydrofolate reductase

Copper-induced conformational change in a marsupial prion protein repeat peptide probed using FTIR spectroscopy

Methyltetrahydrofolate:corrinoid/iron−sulfur Protein Methyltransferase (MeTr): Protonation State of the Ligand and Active-Site Residues

Molecular dynamics simulation of human prion protein including both N-linked oligosaccharides and the GPI anchor

Evolution of vertebrate genes related to prion and Shadoo proteins--clues from comparative genomic analysis

Energetically Most Likely Substrate and Active-Site Protonation Sites and Pathways in the Catalytic Mechanism of Dihydrofolate Reductase

Calculation of a Complete Enzymic Reaction Surface: Reaction and Activation Free Energies for Hydride-Ion Transfer in Dihydrofolate Reductase

CO2 Fixation by Rubisco: Computational Dissection of the Key Steps of Carboxylation, Hydration, and C−C Bond Cleavage

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