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The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinitiesMetal binding to Bacillus subtilis ferrochelatase and interaction between metal sitesThe Carbohydrate-Binding Site in Galectin-3 Is Preorganized To Recognize a Sugarlike Framework of Oxygens: Ultra-High-Resolution Structures and Water DynamicsThe neutron structure of urate oxidase resolves a long-standing mechanistic conundrum and reveals unexpected changes in protonationNMR structure determination of proteins supplemented by quantum chemical calculations: detailed structure of the Ca2+ sites in the EGF34 fragment of protein S.Effect of explicit water molecules on ligand-binding affinities calculated with the MM/GBSA approach.Amino acid oxidation of Candida antarctica lipase B studied by molecular dynamics simulations and site-directed mutagenesis.The protonation status of compound II in myoglobin, studied by a combination of experimental data and quantum chemical calculations: quantum refinement.Which functional groups of the molybdopterin ligand should be considered when modeling the active sites of the molybdenum and tungsten cofactors? A density functional theory study.Combined quantum and molecular mechanics calculations on metalloproteins.Simulation of the isotropic EXAFS spectra for the S2 and S3 structures of the oxygen evolving complex in photosystem II.A large-scale test of free-energy simulation estimates of protein-ligand binding affinities.Structures of the high-valent metal-ion haem-oxygen intermediates in peroxidases, oxygenases and catalases.Converging ligand-binding free energies obtained with free-energy perturbations at the quantum mechanical level.Binding-affinity predictions of HSP90 in the D3R Grand Challenge 2015 with docking, MM/GBSA, QM/MM, and free-energy simulations.Binding free energies in the SAMPL5 octa-acid host-guest challenge calculated with DFT-D3 and CCSD(T).Estimates of ligand-binding affinities supported by quantum mechanical methods.Computational modelling of oxygenation processes in enzymes and biomimetic model complexes.Conformational entropy changes upon lactose binding to the carbohydrate recognition domain of galectin-3.Ligand-Binding Affinity Estimates Supported by Quantum-Mechanical Methods.Starting-Condition Dependence of Order Parameters Derived from Molecular Dynamics Simulations.Effect of Geometry Optimizations on QM-Cluster and QM/MM Studies of Reaction Energies in Proteins.Accurate Reaction Energies in Proteins Obtained by Combining QM/MM and Large QM Calculations.Large Density-Functional and Basis-Set Effects for the DMSO Reductase Catalyzed Oxo-Transfer Reaction.Understanding the Chemistry of Lead at a Molecular Level: The Pb(II) 6s6p Lone Pair Can Be Bisdirected in Proteins.The structures of frataxin oligomers reveal the mechanism for the delivery and detoxification of iron.A combined computational and experimental investigation of the [2Fe-2S] cluster in biotin synthase.An MM/3D-RISM approach for ligand binding affinities.A five-coordinate [2Fe-2S] cluster.Quantum refinement of [FeFe] hydrogenase indicates a dithiomethylamine ligand.Restrained point-charge models for disaccharides.An automatic method to generate force-field parameters for hetero-compounds.On the role of the axial ligand in heme proteins: a theoretical study.Reaction mechanism of porphyrin metallation studied by theoretical methods.How to obtain statistically converged MM/GBSA results.Prediction of activation energies for aromatic oxidation by cytochrome P450.An improved method to predict the entropy term with the MM/PBSA approach.Conformational dependence of charges in protein simulations.O2 Activation in Salicylate 1,2-Dioxygenase: A QM/MM Study Reveals the Role of His162.Secondary bonding interactions in biomimetic [2Fe-2S] clusters.
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description
researcher
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wetenschapper
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name
U Ryde
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U Ryde
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type
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U Ryde
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U Ryde
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U Ryde
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U Ryde
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P106
P31
P496
0000-0001-7653-8489