Ulf Ryde

Ulf Ryde's AcademicInfluence.com Rankings

Ulf Ryde

Biology

#8816

World Rank

#11948

Historical Rank

Cell Biology

#358

World Rank

#368

Historical Rank

Immunology

#511

World Rank

#528

Historical Rank

Genetics

#888

World Rank

#984

Historical Rank

biology Degrees

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Biology

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Ulf Ryde's Published Works

Number of citations in a given year to any of this author's works

Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author

Published Works

The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities (2015) (2289)
Molcas: a program package for computational chemistry. (2003) (1361)
Comparison of methods for deriving atomic charges from the electrostatic potential and moments (1998) (268)
Ligand affinities predicted with the MM/PBSA method: dependence on the simulation method and the force field. (2006) (228)
Protein Flexibility and Conformational Entropy in Ligand Design Targeting the Carbohydrate Recognition Domain of Galectin-3 (2010) (203)
How to obtain statistically converged MM/GBSA results (2009) (191)
Ligand-Binding Affinity Estimates Supported by Quantum-Mechanical Methods. (2016) (184)
Performance of density functionals for first row transition metal systems. (2007) (175)
Structure, strain, and reorganization energy of blue copper models in the protein (2001) (173)
On the Convergence of QM/MM Energies. (2011) (166)
The coordination of the catalytic zinc ion in alcohol dehydrogenase studied by combined quantum-chemical and molecular mechanics calculations (1996) (142)
On the role of the axial ligand in heme proteins: a theoretical study (2004) (142)
How O2 Binds to Heme (2004) (136)
The Normal-Mode Entropy in the MM/GBSA Method: Effect of System Truncation, Buffer Region, and Dielectric Constant (2012) (133)
Structures of the high-valent metal-ion haem-oxygen intermediates in peroxidases, oxygenases and catalases. (2006) (133)
The Carbohydrate-Binding Site in Galectin-3 Is Preorganized To Recognize a Sugarlike Framework of Oxygens: Ultra-High-Resolution Structures and Water Dynamics (2011) (131)
Metal ion enhanced binding of AMD3100 to Asp262 in the CXCR4 receptor. (2003) (130)
Theoretical prediction of the co-c bond strength in cobalamins. (2003) (127)
An MM/3D-RISM approach for ligand binding affinities. (2010) (126)
Quantum mechanical free energy barrier for an enzymatic reaction. (2005) (123)
An improved method to predict the entropy term with the MM/PBSA approach (2009) (122)
The cupric geometry of blue copper proteins is not strained. (1996) (120)
Accurate QM/MM Free Energy Calculations of Enzyme Reactions: Methylation by Catechol O-Methyltransferase. (2005) (119)
Quantum chemistry can locally improve protein crystal structures. (2003) (106)
A QM/MM investigation of the activation and catalytic mechanism of Fe-only hydrogenases. (2007) (106)
Prediction of activation energies for hydrogen abstraction by cytochrome p450. (2006) (103)
Relation between the Structure and Spectroscopic Properties of Blue Copper Proteins (1998) (101)
Carboxylate binding modes in zinc proteins: a theoretical study. (1999) (99)
A comparison of the inner-sphere reorganization energies of cytochromes, iron-sulphur clusters, and blue copper proteins (2001) (99)
Molecular dynamics simulations of alcohol dehydrogenase with a four‐ or five‐coordinate catalytic zinc ion (1995) (96)
Quantum Refinement Does Not Support Dinuclear Copper Sites in Crystal Structures of Particulate Methane Monooxygenase. (2018) (96)
Comparison of Methods to Obtain Force-Field Parameters for Metal Sites. (2011) (91)
Redesign of the coenzyme specificity in L-lactate dehydrogenase from bacillus stearothermophilus using site-directed mutagenesis and media engineering. (1999) (91)
How the Co-C bond is cleaved in coenzyme B12 enzymes: a theoretical study. (2005) (90)
Will molecular dynamics simulations of proteins ever reach equilibrium? (2012) (89)
Quantum Crystallography: Current Developments and Future Perspectives. (2018) (87)
Quantum chemical geometry optimizations in proteins using crystallographic raw data (2002) (87)
The structures of frataxin oligomers reveal the mechanism for the delivery and detoxification of iron. (2006) (86)
How accurate can a force field become? A polarizable multipole model combined with fragment-wise quantum-mechanical calculations. (2009) (86)
Computational modelling of oxygenation processes in enzymes and biomimetic model complexes. (2014) (86)
Combined quantum and molecular mechanics calculations on metalloproteins. (2003) (84)
A fundamental view of enthalpy–entropy compensation (2014) (84)
O2-binding to heme: electronic structure and spectrum of oxyheme, studied by multiconfigurational methods. (2005) (83)
Inner-sphere reorganization energy of iron-sulfur clusters studied with theoretical methods. (2001) (80)
Proceedings of the Chemical Society. June 1958 (1958) (80)
Ligand Affinities Estimated by Quantum Chemical Calculations. (2010) (79)
Influence of the [2Fe]H subcluster environment on the properties of key intermediates in the catalytic cycle of [FeFe] hydrogenases: hints for the rational design of synthetic catalysts. (2009) (79)
Does DFT-D estimate accurate energies for the binding of ligands to metal complexes? (2011) (78)
Do quantum mechanical energies calculated for small models of protein-active sites converge? (2009) (78)
On the role of Glu‐68 in alcohol dehydrogenase (1995) (75)
Free-energy perturbation and quantum mechanical study of SAMPL4 octa-acid host–guest binding energies (2014) (75)
Theoretical study of the electronic spectrum of plastocyanin (1997) (74)
Comparison of end‐point continuum‐solvation methods for the calculation of protein–ligand binding free energies (2012) (74)
On the significance of hydrogen bonds for the discrimination between CO and O2 by myoglobin (1999) (74)
Conformational entropy changes upon lactose binding to the carbohydrate recognition domain of galectin-3 (2009) (73)
Geometry, reduction potential, and reorganization energy of the binuclear Cu(A) site, studied by density functional theory. (2001) (72)
Comparison of MM/GBSA calculations based on explicit and implicit solvent simulations. (2013) (72)
Accurate Reaction Energies in Proteins Obtained by Combining QM/MM and Large QM Calculations. (2013) (72)
How accurate are continuum solvation models for drug-like molecules? (2009) (71)
Review: Studies of ferric heme proteins with highly anisotropic/highly axial low spin (S = 1/2) electron paramagnetic resonance signals with bis‐Histidine and histidine‐methionine axial iron coordination (2009) (71)
Quantum chemical calculations of the reorganization energy of blue‐copper proteins (1998) (70)
Convergence of QM/MM free-energy perturbations based on molecular-mechanics or semiempirical simulations. (2012) (70)
Quantum refinement of [FeFe] hydrogenase indicates a dithiomethylamine ligand. (2010) (69)
Effect of Geometry Optimizations on QM-Cluster and QM/MM Studies of Reaction Energies in Proteins. (2013) (69)
Binding Affinities of Factor Xa Inhibitors Estimated by Thermodynamic Integration and MM/GBSA (2011) (69)
Comparison of the Efficiency of the LIE and MM/GBSA Methods to Calculate Ligand-Binding Energies. (2011) (68)
A combined quantum and molecular mechanical study of the O2 reductive cleavage in the catalytic cycle of multicopper oxidases. (2005) (67)
How Many Conformations Need To Be Sampled To Obtain Converged QM/MM Energies? The Curse of Exponential Averaging. (2017) (65)
Interplay between Conformational Entropy and Solvation Entropy in Protein-Ligand Binding. (2019) (64)
A comparison of different initialization protocols to obtain statistically independent molecular dynamics simulations (2011) (63)
On the role of strain in blue copper proteins (2000) (63)
Sulfoxide, Sulfur, and Nitrogen Oxidation and Dealkylation by Cytochrome P450. (2008) (62)
A Large-Scale Test of Free-Energy Simulation Estimates of Protein-Ligand Binding Affinities (2014) (61)
Protein Influence on Electronic Spectra Modeled by Multipoles and Polarizabilities. (2009) (60)
An automatic method to generate force-field parameters for hetero-compounds. (2003) (58)
QM/MM Calculations on Proteins. (2016) (58)
On the Difference Between Additive and Subtractive QM/MM Calculations (2018) (58)
The importance of porphyrin distortions for the ferrochelatase reaction (2003) (57)
Accurate predictions of nonpolar solvation free energies require explicit consideration of binding-site hydration. (2011) (56)
The influence of axial ligands on the reduction potential of blue copper proteins (1999) (56)
Cobalamins uncovered by modern electronic structure calculations (2009) (55)
Molecular mechanism of lytic polysaccharide monooxygenases† †Electronic supplementary information (ESI) available: Detailed description of the employed computational methods and protein setup. QM and MM energy components and B3LYP energies for most reaction paths. See DOI: 10.1039/c8sc00426a (2018) (54)
Reorganization energy for internal electron transfer in multicopper oxidases. (2011) (53)
Theoretical study of the discrimination between O(2) and CO by myoglobin. (2002) (52)
General Transition-State Force Field for Cytochrome P450 Hydroxylation. (2007) (52)
Prediction of activation energies for aromatic oxidation by cytochrome P450. (2008) (51)
On the relative stability of tetragonal and trigonal Cu(II) complexes with relevance to the blue copper proteins (1998) (50)
A synthetic analogue of Rieske-type [2Fe-2S] clusters. (2008) (50)
Comparison of the Chemical Properties of Iron and Cobalt Porphyrins and Corrins (2003) (48)
Binding affinities in the SAMPL3 trypsin and host–guest blind tests estimated with the MM/PBSA and LIE methods (2012) (48)
Converging ligand‐binding free energies obtained with free‐energy perturbations at the quantum mechanical level (2016) (48)
QM/MM-PBSA method to estimate free energies for reactions in proteins. (2008) (48)
On the possibility of uphill intramolecular electron transfer in multicopper oxidases : electrochemical and quantum chemical study of bilirubin oxidase (2012) (47)
Accurate metal-site structures in proteins obtained by combining experimental data and quantum chemistry. (2007) (47)
Targeting intermediates of [FeFe]-hydrogenase by CO and CN vibrational signatures. (2011) (47)
Theoretical studies of the active-site structure, spectroscopic and thermodynamic properties, and reaction mechanism of multicopper oxidases (2013) (47)
Calculation of protein-ligand interaction energies by a fragmentation approach combining high-level quantum chemistry with classical many-body effects. (2009) (47)
Targeting the reactive intermediate in polysaccharide monooxygenases (2017) (46)
Protonation States of Homocitrate and Nearby Residues in Nitrogenase Studied by Computational Methods and Quantum Refinement. (2017) (46)
The protonation status of compound II in myoglobin, studied by a combination of experimental data and quantum chemical calculations: quantum refinement. (2004) (45)
Metal binding to Bacillus subtilis ferrochelatase and interaction between metal sites (2003) (45)
Reaction mechanism of porphyrin metallation studied by theoretical methods. (2005) (44)
Combined computational and crystallographic study of the oxidised states of [NiFe] hydrogenase (2006) (44)
A theoretical study of the copper–cysteine bond in blue copper proteins (2001) (43)
Comparison of QM/MM Methods To Obtain Ligand-Binding Free Energies. (2017) (43)
Quantum refinement - a combination of quantum chemistry and protein crystallography. (2003) (43)
The role of axial ligands for the structure and function of chlorophylls (2006) (42)
Accurate calculations of geometries and singlet-triplet energy differences for active-site models of [NiFe] hydrogenase. (2014) (42)
Dynamics of water molecules in the active-site cavity of human cytochromes P450. (2007) (41)
Structural insights into the active-ready form of [FeFe]-hydrogenase and mechanistic details of its inhibition by carbon monoxide. (2007) (41)
Structure of reduced and oxidized manganese superoxide dismutase: a combined computational and experimental approach. (2006) (40)
Binding affinities by alchemical perturbation using QM/MM with a large QM system and polarizable MM model (2015) (40)
Binding-affinity predictions of HSP90 in the D3R Grand Challenge 2015 with docking, MM/GBSA, QM/MM, and free-energy simulations (2016) (40)
The crystal structure of peroxymyoglobin generated through cryoradiolytic reduction of myoglobin compound III during data collection. (2008) (39)
Reaction mechanism of manganese superoxide dismutase studied by combined quantum and molecular mechanical calculations and multiconfigurational methods. (2009) (39)
Protein strain in blue copper proteins studied by free energy perturbations (1999) (39)
Multireference ab initio calculations of g tensors for trinuclear copper clusters in multicopper oxidases. (2010) (38)
Fast Generation of Broken-Symmetry States in a Large System Including Multiple Iron-Sulfur Assemblies: Investigation of QM/MM Energies, Clusters Charges, and Spin Populations (2010) (38)
Starting-Condition Dependence of Order Parameters Derived from Molecular Dynamics Simulations. (2010) (38)
The axial N-base has minor influence on Co-C bond cleavage in cobalamins (2002) (38)
Protonation status of metal-bound ligands can be determined by quantum refinement. (2004) (38)
Influence of the protein and DFT method on the broken‐symmetry and spin states in nitrogenase (2018) (37)
Multireference ab initio calculations on reaction intermediates of the multicopper oxidases. (2006) (37)
Unraveling the similarity of the photoabsorption of deprotonated p-coumaric acid in the gas phase and within the photoactive yellow protein. (2011) (37)
Large Density-Functional and Basis-Set Effects for the DMSO Reductase Catalyzed Oxo-Transfer Reaction. (2013) (37)
The reaction mechanism of iron and manganese superoxide dismutases studied by theoretical calculations (2006) (36)
Protonation and Reduction of the FeMo Cluster in Nitrogenase Studied by Quantum Mechanics/Molecular Mechanics (QM/MM) Calculations. (2018) (36)
Extremely large differences in DFT energies for nitrogenase models. (2019) (36)
Protonation states of intermediates in the reaction mechanism of [NiFe] hydrogenase studied by computational methods (2016) (36)
Mechanistic and physiological implications of the interplay among iron-sulfur clusters in [FeFe]-hydrogenases. A QM/MM perspective. (2011) (36)
Conversion of homocysteine to methionine by methionine synthase: a density functional study. (2003) (35)
Reduction potentials and acidity constants of Mn superoxide dismutase calculated by QM/MM free-energy methods. (2011) (35)
Identification of the peroxy adduct in multicopper oxidases by a combination of computational chemistry and extended X-ray absorption fine-structure measurements. (2007) (34)
A QM/MM study of the binding of RAPTA ligands to cathepsin B (2011) (34)
Proton Transfer at Metal Sites in Proteins Studied by Quantum Mechanical Free-Energy Perturbations. (2008) (33)
Structural and photoluminescence properties of excited state intramolecular proton transfer capable compounds-potential emissive and electron transport materials. (2006) (33)
Comparison of overlap-based models for approximating the exchange-repulsion energy. (2006) (32)
Large equatorial ligand effects on C-H bond activation by nonheme iron(IV)-oxo complexes. (2014) (31)
Accuracy of distributed multipoles and polarizabilities: Comparison between the LoProp and MpProp models (2007) (31)
Functionally relevant interplay between the Fe(4)S(4) cluster and CN(-) ligands in the active site of [FeFe]-hydrogenases. (2010) (31)
Conformational Entropies and Order Parameters: Convergence, Reproducibility, and Transferability. (2014) (31)
A semiempirical approach to ligand‐binding affinities: Dependence on the Hamiltonian and corrections (2012) (31)
H2 binding to the active site of [NiFe] hydrogenase studied by multiconfigurational and coupled-cluster methods. (2017) (29)
Simulation of the isotropic EXAFS spectra for the S2 and S3 structures of the oxygen evolving complex in photosystem II (2015) (29)
The structure of sitting-atop complexes of metalloporphyrins studied by theoretical methods. (2004) (29)
Protonation of the proximal histidine ligand in heme peroxidases. (2008) (28)
Nonpolar Solvation Free Energies of Protein-Ligand Complexes. (2010) (27)
Transition-State Docking of Flunitrazepam and Progesterone in Cytochrome P450. (2008) (27)
Prediction and rationalization of the pH dependence of the activity and stability of family 11 xylanases. (2007) (27)
Effect of explicit water molecules on ligand-binding affinities calculated with the MM/GBSA approach (2014) (27)
Theoretical EXAFS studies of a model of the oxygen-evolving complex of photosystem II obtained with the quantum cluster approach (2013) (25)
The Neutron Structure of Urate Oxidase Resolves a Long-Standing Mechanistic Conundrum and Reveals Unexpected Changes in Protonation (2014) (25)
What Is the Structure of the E4 Intermediate in Nitrogenase? (2020) (25)
The coordination chemistry of the structural zinc ion in alcohol dehydrogenase studied by ab initio quantum chemical calculations (1996) (25)
Relative Ligand-Binding Free Energies Calculated from Multiple Short QM/MM MD Simulations. (2018) (24)
Reaction mechanism of formate dehydrogenase studied by computational methods (2018) (24)
Can the protonation state of histidine residues be determined from molecular dynamics simulations (2012) (24)
Binding free energies in the SAMPL5 octa-acid host–guest challenge calculated with DFT-D3 and CCSD(T) (2016) (24)
Erratum to “O2-binding to heme: electronic structure and spectrum of oxyheme, studied by multiconfigurational methods” [J. Inorg. Biochem. 99(1) (2004) 45–54] (2005) (23)
Importance of proximal hydrogen bonds in haem proteins (2003) (23)
Theoretical Study of the Structural and Spectroscopic Properties of Stellacyanin (1998) (23)
Reductive cleavage of the O-O bond in multicopper oxidases: a QM/MM and QM study. (2011) (23)
Magnetic Properties of [FeFe]-Hydrogenases: A Theoretical Investigation Based on Extended QM and QM/MM Models of the H-Cluster and Its Surroundings (2011) (23)
Multiscale Modelling of Lytic Polysaccharide Monooxygenases (2016) (22)
Interpretation of EXAFS spectra for sitting-atop complexes with the help of computational methods (2006) (22)
Conformational dependence of charges in protein simulations (2009) (22)
Mechanism of hydrogen peroxide formation by lytic polysaccharide monooxygenase† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c8sc03980a (2018) (22)
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 (2009) (22)
Catalytic Cycle of Multicopper Oxidases Studied by Combined Quantum- and Molecular-Mechanical Free-Energy Perturbation Methods. (2015) (21)
EXAFS structure refinement supplemented by computational chemistry (2006) (21)
Implicit versus explicit solvent in free energy calculations of enzyme catalysis: Methyl transfer catalyzed by catechol O-methyltransferase. (2006) (21)
A quantum-mechanical study of the reaction mechanism of sulfite oxidase (2014) (21)
Accuracy of typical approximations in classical models of intermolecular polarization. (2008) (21)
Secondary bonding interactions in biomimetic [2Fe-2S] clusters. (2008) (20)
The coordination chemistry of the catalytic zinc ion in alcohol dehydrogenase studied by ab initio quantum chemical calculations (1994) (20)
A Computational Comparison of Oxygen Atom Transfer Catalyzed by Dimethyl Sulfoxide Reductase with Mo and W (2015) (20)
Theoretical study of structure of catalytic copper site in nitrite reductase (2005) (20)
Improving the Efficiency of Protein-Ligand Binding Free-Energy Calculations by System Truncation. (2012) (20)
Estimates of ligand-binding affinities supported by quantum mechanical methods (2010) (19)
Coupled-cluster interaction energies for 200-atom host-guest systems. (2014) (19)
Host-Guest Relative Binding Affinities at Density-Functional Theory Level from Semiempirical Molecular Dynamics Simulations. (2019) (18)
Comparison of the active-site design of molybdenum oxo-transfer enzymes by quantum mechanical calculations. (2014) (18)
Lactam hydrolysis catalyzed by mononuclear metallo-beta-lactamases: a density functional study (2003) (18)
The structure and function of blue copper proteins (2001) (18)
NMR structure determination of proteins supplemented by quantum chemical calculations: Detailed structure of the Ca2+ sites in the EGF34 fragment of protein S (2005) (18)
Multiscale modeling of the active site of [Fe] hydrogenase: the H₂ binding site in open and closed protein conformations. (2015) (17)
Binding of Benzylpenicillin to Metallo-β-lactamase: A QM/MM Study (2004) (17)
Quantum-mechanical studies of reactions performed by cytochrome P450 enzymes (2012) (16)
Isocyanide in biochemistry? A theoretical investigation of the electronic effects and energetics of cyanide ligand protonation in [FeFe]-hydrogenases. (2011) (16)
On the significance of the trigger reaction in the action of the calicheamicin γ1I anti-cancer drug (1997) (16)
QM/MM study of the reaction mechanism of sulfite oxidase (2018) (16)
Ab Initio Calculations of Electric Field Gradients in Cadmium Complexes (1996) (16)
A comparative reactivity study of microperoxidases based on hemin, mesohemin and deuterohemin. (2005) (16)
Predicting Relative Binding Affinity Using Nonequilibrium QM/MM Simulations. (2018) (15)
Geometry and Electronic Structure of the P-Cluster in Nitrogenase Studied by Combined Quantum Mechanical and Molecular Mechanical Calculations and Quantum Refinement. (2019) (15)
The Influence of X‐Rays on the Structural Studies of Peroxide‐Derived Myoglobin Intermediates (2008) (15)
Theoretical 57Fe Mössbauer spectroscopy: isomer shifts of [Fe]-hydrogenase intermediates. (2014) (15)
Conformational Dependence of Isotropic Polarizabilities. (2011) (15)
Amino acid oxidation of Candida antarctica lipase B studied by molecular dynamics simulations and site-directed mutagenesis. (2013) (15)
Structure and Energetics of Ligand–Fluorine Interactions with Galectin‐3 Backbone and Side‐Chain Amides: Insight into Solvation Effects and Multipolar Interactions (2019) (15)
A five-coordinate [2Fe-2S] cluster. (2010) (14)
Comparison of chemical properties of iron, cobalt, and nickel porphyrins, corrins, and hydrocorphins (2005) (14)
Assessing the stability of free-energy perturbation calculations by performing variations in the method (2018) (14)
Protonation states of intermediates in the reaction mechanism of [NiFe] hydrogenase studied by computational methods (2016) (14)
GEOMETRIC AND ELECTRONIC STRUCTURE OF CO(II)-SUBSTITUTED AZURIN (1999) (13)
Entropy–Entropy Compensation between the Protein, Ligand, and Solvent Degrees of Freedom Fine-Tunes Affinity in Ligand Binding to Galectin-3C (2021) (13)
Does the DFT Self-Interaction Error Affect Energies Calculated in Proteins with Large QM Systems? (2016) (13)
Binding free energies in the SAMPL6 octa-acid host–guest challenge calculated with MM and QM methods (2018) (12)
Refinement of protein structures using a combination of quantum-mechanical calculations with neutron and X-ray crystallographic data (2019) (12)
O2 Activation in Salicylate 1,2-Dioxygenase: A QM/MM Study Reveals the Role of His162. (2016) (12)
QM/MM study of the insertion of metal ion into protoporphyrin IX by ferrochelatase. (2009) (12)
A DFT investigation on structural and redox properties of a synthetic Fe6S6 assembly closely related to the [FeFe]-hydrogenases active site (2008) (12)
Exploration of H2 binding to the [NiFe]-hydrogenase active site with multiconfigurational density functional theory. (2017) (11)
On the Use of Interaction Entropy and Related Methods to Estimate Binding Entropies (2021) (11)
Probing the effects of one-electron reduction and protonation on the electronic properties of the Fe-S clusters in the active-ready form of [FeFe]-hydrogenases. A QM/MM investigation. (2011) (11)
The active-site metal coordination geometry of cadmium-substituted alcohol dehydrogenase (1997) (11)
Transferability of conformational dependent charges from protein simulations (2012) (11)
Are crystallographic B-factors suitable for calculating protein conformational entropy? (2019) (11)
Binding affinities of the farnesoid X receptor in the D3R Grand Challenge 2 estimated by free-energy perturbation and docking (2017) (10)
Insight into the reaction mechanism of lipoyl synthase: a QM/MM study (2017) (10)
Restrained point‐charge models for disaccharides (2002) (9)
Arguments for a narrow species concept in Rubus sect. Corylifolii (2011) (9)
Critical evaluation of a crystal structure of nitrogenase with bound N2 ligands (2021) (9)
Does the crystal structure of vanadium nitrogenase contain a reaction intermediate? Evidence from quantum refinement (2020) (9)
A combined computational and experimental investigation of the [2Fe–2S] cluster in biotin synthase (2009) (8)
A thiocarbonate sink on the enzymatic energy landscape of aerobic CO oxidation? Answers from DFT and QM/MM models of Mo Cu CO-dehydrogenases (2019) (8)
N2H2 binding to the nitrogenase FeMo cluster studied by QM/MM methods (2020) (8)
Putative reaction mechanism of nitrogenase after dissociation of a sulfide ligand (2020) (8)
Why does sulfite reductase employ siroheme? (2019) (8)
Substituted polyfluoroaryl interactions with an arginine side chain in galectin-3 are governed by steric-, desolvation and electronic conjugation effects. (2019) (8)
Supporting Information Mechanism of hydrogen peroxide formation by lytic polysaccharide monooxygenase (2019) (7)
Molecular mechanism of lytic polysaccharide monooxygenases (2018) (7)
A novel mechanism of heme degradation to biliverdin studied by QM/MM and QM calculations. (2018) (7)
Understanding the Chemistry of Lead at a Molecular Level: The Pb(II) 6s6p Lone Pair Can Be Bisdirected in Proteins. (2013) (7)
How are hydrogen bonds modified by metal binding? (2013) (7)
drogen peroxide formation by lytic polysaccharide monooxygenase † (2018) (7)
Quantum Mechanics in Structure‐Based Ligand Design (2012) (7)
Thermodynamically Favourable States in the Reaction of Nitrogenase without Dissociation of any Sulfide Ligand (2022) (6)
QM/MM Study of the Conversion of Oxophlorin into Verdoheme by Heme Oxygenase. (2017) (6)
Proton Transfer Pathways in Nitrogenase with and without Dissociated S2B (2022) (6)
Higher Flexibility of Glu-172 Explains the Unusual Stereospecificity of Glyoxalase I. (2018) (6)
Nuclear Quadrupole Interactions in Cadmium Complexes: Semiempirical and ab initio Calculations (1999) (6)
Can MM/GBSA calculations be sped up by system truncation? (2018) (5)
Is density functional theory accurate for lytic polysaccharide monooxygenase enzymes? (2019) (5)
Water structure in solution and crystal molecular dynamics simulations compared to protein crystal structures (2020) (5)
Effect of covalent links on the structure, spectra, and redox properties of myeloperoxidase--a density functional study. (2008) (5)
Catalytic mechanism of human glyoxalase i studied by quantum-mechanical cluster calculations (2016) (5)
Combining crystallography with quantum mechanics. (2021) (5)
On the role of covalent strain in protein function (2002) (4)
QM/MM Study of the Catalytic Reaction of Myrosinase; Importance of Assigning Proper Protonation States of Active-Site Residues (2021) (4)
Quantum refinement with multiple conformations: application to the P-cluster in nitrogenase (2020) (4)
Quantum refinement — a method to determine protonation and oxidation states of metal sites in protein crystal structures (2003) (4)
Comparison of the accuracy of DFT methods for reactions with relevance to nitrogenase (2021) (4)
Effect of the protein ligand in DMSO reductase studied by computational methods. (2017) (4)
QM/MM study of the binding of H2 to MoCu CO dehydrogenase: development and applications of improved H2 van der Waals parameters (2021) (3)
Quantum-refinement studies of the bidentate ligand of V‑nitrogenase and the protonation state of CO-inhibited Mo‑nitrogenase. (2021) (3)
Theoretical Insights into the Aerobic Hydrogenase Activity of Molybdenum–Copper CO Dehydrogenase (2019) (3)
Automated orientation of water molecules in neutron crystallographic structures of proteins. (2020) (3)
Benchmark Study of Redox Potential Calculations for Iron–Sulfur Clusters in Proteins (2022) (3)
Computational Modelling of Oxygenation Processes in Enzymes and Biomimetic Model Complexes (2014) (3)
Neutron structures of Leishmania mexicana triosephosphate isomerase in complex with reaction-intermediate mimics shed light on the proton-shuttling steps (2021) (3)
Computational Studies of Molybdenum and Tungsten Enzymes (2016) (3)
Molecular orbital theory. (2003) (3)
QM/MM study of the stereospecific proton exchange of glutathiohydroxyacetone by glyoxalase I (2019) (3)
QM/MM Study of Partial Dissociation of S2B for the E2 Intermediate of Nitrogenase (2022) (3)
The correlation between structure and spectra of blue copper proteins (1997) (3)
How O 2 Binds to Heme (2004) (3)
Structure and energetics of ligand-fluorine interactions with galectin-3 backbone and side-chain amides - insight into solvation effects and multipolar interactions. (2019) (2)
Hybrids between Rubus idaeus and Rubus sect. Corylifolii and their relation to R. pruinosus and R. rosanthus (2021) (2)
fragHAR: towards ab initio quantum-crystallographic X-ray structure refinement for polypeptides and proteins (2020) (2)
Unraveling the Reaction Mechanism of Mo/Cu CO Dehydrogenase Using QM/MM Calculations (2022) (2)
Exploring ligand dynamics in protein crystal structures with ensemble refinement (2021) (2)
Genetic analysis shows that Rubus vikensis is a distinct species with a disjunct distribution (2010) (2)
Quantum Mechanical/Molecular Mechanical (QM/MM) Methods and Applictions in Bioinorganic Chemistry (2009) (2)
Rubus sect. Corylifolii in the province of Halland, SW Sweden (2009) (2)
Exploration of H 2 binding to the [ NiFe ]-hydrogenase active site with multiconfigurational density functional theory (2017) (2)
Importance of the iron-sulfur component and of the siroheme modification in the resting state of sulfite reductase. (2019) (2)
The Influence of X-Rays on the Structural Studies of Peroxide-Derived Myoglobin Intermediates (2009) (1)
Correction: Mechanism of hydrogen peroxide formation by lytic polysaccharide monooxygenase (2019) (1)
Frontispiece: Quantum Crystallography: Current Developments and Future Perspectives (2018) (1)
A comparison of the tetrapyrrole cofactors in nature and their tuning by axial ligands (2008) (1)
Computationally enhanced X-ray diffraction analysis of a gold(III) complex interacting with the human telomeric DNA G-quadruplex. Unravelling non-unique ligand positioning. (2022) (1)
QM/MM study of the conversion of biliverdin into verdoheme by heme oxygenase (2019) (1)
Can System Truncation Speed up Ligand-Binding Calculations with Periodic Free-Energy Simulations? (2017) (1)
Quantum Mechanics/Molecular Mechanics Study of the Reaction Mechanism of Glyoxalase I. (2020) (1)
Rubus sordirosanthus in Halland, southwest Sweden (2010) (1)
Identification of possible tworeactant sources of oscillations in the Calvin photosynthesis cycle and ancillary pathways (2004) (1)
Structure of the intermediates in the myoglobin-peroxide reaction (2005) (1)
Can Water Act as a Nucleophile in CO Oxidation Catalysed by Mo/Cu CO‐Dehydrogenase? Answers from Theory (2022) (1)
Two-Substrate Glyoxalase I Mechanism: A Quantum Mechanics/Molecular Mechanics Study. (2020) (1)
Syddansk Universitet Theoretical 57 Fe Mössbauer spectroscopy : isomer shifts of [ Fe ]-hydrogenase intermediates (2017) (0)
CCDC 685962: Experimental Crystal Structure Determination (2008) (0)
Targeting the reactive intermediate in polysaccharide monooxygenases (2017) (0)
Proteins, Blue Copper: Electronic Spectra (2002) (0)
Inside Cover: A Synthetic Analogue of Rieske-Type [2Fe-2S] Clusters (Angew. Chem. Int. Ed. 49/2008) (2008) (0)
Mechanism of Fe-only hydrogenases studied by QM/MMn methods (2007) (0)
CCDC 692369: Experimental Crystal Structure Determination (2009) (0)
Molecular Dynamics and QM / MM Investigations on a 2 , 3-Dioxygenase Metalloenzyme (2016) (0)
An automated hydrogen orientation procedure for neutron protein crystallography (2021) (0)
Cyanide ligands in [FeFe]-hydrogenases active site: dissecting their role in biological H2 evolution. (2011) (0)
Automated Orientation of Water Molecules in Neutron Structures of Proteins (2021) (0)
On the mechanistic origin of damped oscillations in biochemical reaction systems (2018) (0)
A quantum-mechanical study of the reaction mechanism of sulfite oxidase (2014) (0)
Can 57Fe Mössbauer isomer shifts be calculated accurately without fitting? Isomer shifts for [Fe]-Hydrogenase Intermediates (2013) (0)
How general is the effect of the bulkiness of organic ligands on the basicity of metal-organic catalysts? H2-evolving Mo oxides/sulphides as case studies. (2022) (0)
Improving identification and validation of water molecules in protein crystal structures with molecular dynamics simulations (2019) (0)
CCDC 692367: Experimental Crystal Structure Determination (2009) (0)
Refinement of protein structures using a combination of quantum-mechanical calculations with neutron and X-ray crystallographic data. Corrigendum (2020) (0)
Obtaining accurate structures and energies with QM/MM (2020) (0)
CCDC 685961: Experimental Crystal Structure Determination (2008) (0)
Insight into the reaction mechanism of lipoyl synthase: a QM/MM study (2017) (0)
QM/MM study of the reaction mechanism of sulfite oxidase (2018) (0)
Hybrids between Rubus caesius and Rubus sect. Corylifolii (Rosaceae) and their relation to R. cyclomorphus , R. tiliaster , R. glauciformis , R. slesvicensis and R. firmus (2022) (0)
Quantum Mechanical Calculations of Redox Potentials of the Metal Clusters in Nitrogenase (2022) (0)
How are hydrogen bonds modified by metal binding? (2013) (0)
MS03 Enzymes: Structures and Mechanisms (2007) (0)
The neutron structure of Leishmania mexicana triose phosphate isomerase with transition state mimics reveals general base catalyst (2019) (0)
A computational study of the reaction mechanism and stereospecificity of dihydropyrimidinase. (2023) (0)
Quantum Mechanics/Molecular Mechanics Study of theReaction Mechanism of Glyoxalase I (2020) (0)
CCDC 685965: Experimental Crystal Structure Determination (2008) (0)
Comparison of Grand Canonical and Conventional Molecular Dynamics Simulation Methods for Protein-Bound Water Networks (2022) (0)
Reaction mechanism of formate dehydrogenase studied by computational methods (2018) (0)
Surprising protonation states in urate oxidase – combining X-ray and neutron crystallography with QM/MM (2012) (0)
Mechanism of Bilirubin Oxidase: Fabrication and Characterization of Efficient Biocathode (2010) (0)
HOT ARTICLES : Matrix infrared spectroscopic and density functional theoretical investigations on thorium and uranium atom reactions with dimethyl ether (2011) (0)
Can the results of quantum refinement be improved with a continuum-solvation model? (2021) (0)
Comparison of force fields to study the zinc-finger containing protein NPL4, a target for Antabuse in cancer therapy (2023) (0)
Crystal Structure of B. subilis ferrochelatase with Zn(2+) bound at the active site. (2003) (0)
Catalytic Reaction Mechanism of Glyoxalase II, A Member of the Glyoxalase System Responsible for Detoxifying Methylglyoxal (2022) (0)
Crystal Structure of Ferrochelatase with Cadmium bound at active site (2003) (0)
Backbone and methyl chemical shift assignments, relaxation data and orderparameters of Galectin-3C in complex with ortho-fluoroaryltriazolegalactopyranosyl 1-thio-D-glucopyranoside derivative (2020) (0)
Human galectin-3 in complex with a benzamido-N-acetyllactoseamine inhibitor (2010) (0)
Molecular dynamic simulations of alcohol dehydrogenase with a four-or five-coordinate catalytic zinc ion by Ulf Ryde (2017) (0)
Histidine oxidation in lytic polysaccharide monooxygenase (2023) (0)
Structural basis of the iron storage and delivery functions of frataxin (2007) (0)
CCDC 685960: Experimental Crystal Structure Determination (2008) (0)
Substituted poly fl uoroaryl interactions with an arginine side chain in galectin-3 are governed by steric-, desolvation and electronic conjugation e ff ects † (2019) (0)
Quantum refinement of X-ray and neutron protein crystal structures (2018) (0)
Redox and electronic properties of the entire iron–sulfur cluster chain in [FeFe]-hydrogenases: a QM/MM investigation (2011) (0)
Understanding the toxicology of lead at a molecular level: Pb(II) 6s lone pair can be bisdirected in proteins (2014) (0)
CCDC 685964: Experimental Crystal Structure Determination (2008) (0)

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What Schools Are Affiliated With Ulf Ryde?

Ulf Ryde is affiliated with the following schools:

Technical University of Denmark
Uppsala University
Royal Veterinary and Agricultural University
University of Gothenburg
Lund University
University of Copenhagen

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