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List of works by Ulf Ryde

(2963) Proposal to reject the name <i>Rubus pseudoidaeus</i> (<i>Rosaceae</i>)

scientific article published in 2023

A QM/MM investigation of the activation and catalytic mechanism of Fe-only hydrogenases

scientific article published on 29 June 2007

A QM/MM study of the binding of RAPTA ligands to cathepsin B

scientific article published on 24 June 2011

A combined computational and experimental investigation of the [2Fe-2S] cluster in biotin synthase.

scientific article published on 19 September 2009

A comparison of different initialization protocols to obtain statistically independent molecular dynamics simulations ⬇️

scientific article published on January 30, 2011

A five-coordinate [2Fe-2S] cluster.

scientific article published in July 2010

A large-scale test of free-energy simulation estimates of protein-ligand binding affinities.

scientific article

A novel mechanism of heme degradation to biliverdin studied by QM/MM and QM calculations

scientific article published on 01 June 2018

A quantum-mechanical study of the reaction mechanism of sulfite oxidase

scientific article published on 24 June 2014

A semiempirical approach to ligand-binding affinities: dependence on the Hamiltonian and corrections

scientific article published on 07 March 2012

A synthetic analogue of Rieske-type [2Fe-2S] clusters

scientific article published on 01 January 2008

Accuracy of distributed multipoles and polarizabilities: Comparison between the LoProp and MpProp models

scientific article published in 2007

Accuracy of typical approximations in classical models of intermolecular polarization

scientific article published on 01 January 2008

Accurate QM/MM Free Energy Calculations of Enzyme Reactions:  Methylation by Catechol O-Methyltransferase

scientific article published on 01 November 2005

Accurate Reaction Energies in Proteins Obtained by Combining QM/MM and Large QM Calculations

scientific article published on 8 November 2012

Accurate calculations of geometries and singlet–triplet energy differences for active-site models of [NiFe] hydrogenase

scientific article published in 2014

Accurate predictions of nonpolar solvation free energies require explicit consideration of binding-site hydration

scientific article published on 29 July 2011

Amino acid oxidation of Candida antarctica lipase B studied by molecular dynamics simulations and site-directed mutagenesis.

scientific article

An MM/3D-RISM approach for ligand binding affinities.

scientific article published in July 2010

An automatic method to generate force-field parameters for hetero-compounds.

scientific article

An improved method to predict the entropy term with the MM/PBSA approach.

scientific article

Are crystallographic B-factors suitable for calculating protein conformational entropy?

scientific article published on 01 August 2019

Assessing the stability of free-energy perturbation calculations by performing variations in the method.

scientific article

Benchmark Study of Redox Potential Calculations for Iron–Sulfur Clusters in Proteins

scientific article published in 2022

Binding affinities by alchemical perturbation using QM/MM with a large QM system and polarizable MM model

scientific article published on 17 August 2015

Binding affinities in the SAMPL3 trypsin and host–guest blind tests estimated with the MM/PBSA and LIE methods

article

Binding affinities of factor Xa inhibitors estimated by thermodynamic integration and MM/GBSA.

scientific article published on 18 March 2011

Binding affinities of the farnesoid X receptor in the D3R Grand Challenge 2 estimated by free-energy perturbation and docking.

scientific article published on 6 September 2017

Binding free energies in the SAMPL5 octa-acid host-guest challenge calculated with DFT-D3 and CCSD(T).

scientific article published on 06 September 2016

Binding free energies in the SAMPL6 octa-acid host-guest challenge calculated with MM and QM methods

scientific article published on 10 September 2018

Binding-affinity predictions of HSP90 in the D3R Grand Challenge 2015 with docking, MM/GBSA, QM/MM, and free-energy simulations

scientific article published on 26 August 2016

Calculation of protein-ligand interaction energies by a fragmentation approach combining high-level quantum chemistry with classical many-body effects

scientific article published on 01 August 2009

Can MM/GBSA calculations be sped up by system truncation?

scientific article published on 26 November 2017

Can System Truncation Speed up Ligand-Binding Calculations with Periodic Free-Energy Simulations?

scientific article

Catalytic Cycle of Multicopper Oxidases Studied by Combined Quantum- and Molecular-Mechanical Free-Energy Perturbation Methods

scientific article published on 17 June 2015

Combined quantum and molecular mechanics calculations on metalloproteins.

scientific article

Comparison of Methods to Obtain Force-Field Parameters for Metal Sites

scientific article published on 20 July 2011

Comparison of QM/MM Methods To Obtain Ligand-Binding Free Energies.

scientific article published on 29 March 2017

Comparison of end-point continuum-solvation methods for the calculation of protein-ligand binding free energies

scientific article published on 13 February 2012

Comparison of overlap-based models for approximating the exchange-repulsion energy

scientific article published on 01 June 2006

Comparison of the Chemical Properties of Iron and Cobalt Porphyrins and Corrins ⬇️

scientific article published on May 9, 2003

Comparison of the Efficiency of the LIE and MM/GBSA Methods to Calculate Ligand-Binding Energies

scientific article published on 19 October 2011

Comparison of the active-site design of molybdenum oxo-transfer enzymes by quantum mechanical calculations

scientific article published on 05 November 2014

Computational modelling of oxygenation processes in enzymes and biomimetic model complexes

scientific article

Conformational Dependence of Isotropic Polarizabilities

scientific article published on 11 April 2011

Conformational Entropies and Order Parameters: Convergence, Reproducibility, and Transferability

scientific article published on 01 January 2014

Conformational dependence of charges in protein simulations.

scientific article

Conformational entropy changes upon lactose binding to the carbohydrate recognition domain of galectin-3.

scientific article

Convergence of QM/MM free-energy perturbations based on molecular-mechanics or semiempirical simulations

scientific article published on 13 July 2012

Converging ligand-binding free energies obtained with free-energy perturbations at the quantum mechanical level.

scientific article published on 27 April 2016

Conversion of Homocysteine to Methionine by Methionine Synthase: A Density Functional Study ⬇️

scientific article published on November 19, 2003

Coupled-cluster interaction energies for 200-atom host-guest systems

scientific article published on 26 September 2014

Do quantum mechanical energies calculated for small models of protein-active sites converge?

scientific article

Does DFT-D estimate accurate energies for the binding of ligands to metal complexes?

scientific article published on 19 August 2011

Does the DFT Self-Interaction Error Affect Energies Calculated in Proteins with Large QM Systems?

scientific article published on 17 October 2016

Dynamics of Water Molecules in the Active-Site Cavity of Human Cytochromes P450

article

Effect of Geometry Optimizations on QM-Cluster and QM/MM Studies of Reaction Energies in Proteins

scientific article published on 22 August 2013

Effect of explicit water molecules on ligand-binding affinities calculated with the MM/GBSA approach.

scientific article

Estimates of ligand-binding affinities supported by quantum mechanical methods.

scientific article published on 28 January 2010

Exploration of H2 binding to the [NiFe]-hydrogenase active site with multiconfigurational density functional theory.

scientific article

Exploring ligand dynamics in protein crystal structures with ensemble refinement

scientific article published on 29 July 2021

Extremely large differences in DFT energies for nitrogenase models

scientific article published on 01 January 2019

Free-energy perturbation and quantum mechanical study of SAMPL4 octa-acid host-guest binding energies

scientific article published on 04 April 2014

Functionally relevant interplay between the Fe(4)S(4) cluster and CN(-) ligands in the active site of [FeFe]-hydrogenases.

scientific article

General Transition-State Force Field for Cytochrome P450 Hydroxylation

scientific article published on 01 September 2007

Geometry and Electronic Structure of the P-Cluster in Nitrogenase Studied by Combined Quantum Mechanical and Molecular Mechanical Calculations and Quantum Refinement

scientific article published on 08 July 2019

H2 binding to the active site of [NiFe] hydrogenase studied by multiconfigurational and coupled-cluster methods

scientific article published on 01 April 2017

Higher Flexibility of Glu-172 Explains the Unusual Stereospecificity of Glyoxalase I

scientific article published on 10 April 2018

Host-Guest Relative Binding Affinities at Density-Functional Theory Level from Semiempirical Molecular Dynamics Simulations

scientific article published on 13 March 2019

How Many Conformations Need To Be Sampled To Obtain Converged QM/MM Energies? The Curse of Exponential Averaging

scientific article published on 12 October 2017

How accurate are continuum solvation models for drug-like molecules?

scientific article

How accurate can a force field become? A polarizable multipole model combined with fragment-wise quantum-mechanical calculations

scientific article published on 01 January 2009

How to obtain statistically converged MM/GBSA results.

scientific article published in March 2010

Hybrids between Rubus caesius and Rubus sect. Corylifolii (Rosaceae) and their relation to R. cyclomorphus , R. tiliaster , R. glauciformis , R. slesvicensis and R. firmus ⬇️

scientific article published on 30 November 2022

Identification of the peroxy adduct in multicopper oxidases by a combination of computational chemistry and extended X-ray absorption fine-structure measurements

scientific article published on 01 January 2007

Implicit versus explicit solvent in free energy calculations of enzyme catalysis: Methyl transfer catalyzed by catechol O-methyltransferase

scientific article published on 01 May 2006

Improving the Efficiency of Protein-Ligand Binding Free-Energy Calculations by System Truncation

scientific article published on 12 March 2012

Interplay between Conformational Entropy and Solvation Entropy in Protein-Ligand Binding

scientific article published on 23 January 2019

Is density functional theory accurate for lytic polysaccharide monooxygenase enzymes?

scientific article published on 01 February 2020

Isocyanide in biochemistry? A theoretical investigation of the electronic effects and energetics of cyanide ligand protonation in [FeFe]-hydrogenases

scientific article published on 12 January 2011

Large Density-Functional and Basis-Set Effects for the DMSO Reductase Catalyzed Oxo-Transfer Reaction.

scientific article published on 6 February 2013

Large equatorial ligand effects on C-H bond activation by nonheme iron(IV)-oxo complexes

scientific article published on 04 February 2014

Ligand Affinities Estimated by Quantum Chemical Calculations

scientific article

Ligand affinities predicted with the MM/PBSA method: dependence on the simulation method and the force field.

scientific article published in November 2006

Ligand-Binding Affinity Estimates Supported by Quantum-Mechanical Methods.

scientific article published on 14 April 2016

Mechanism of hydrogen peroxide formation by lytic polysaccharide monooxygenase.

scientific article

Mechanistic and Physiological Implications of the Interplay among Iron–Sulfur Clusters in [FeFe]-Hydrogenases. A QM/MM Perspective ⬇️

scientific article published on October 26, 2011

Metal binding to Bacillus subtilis ferrochelatase and interaction between metal sites

scientific article (publication date: April 2003)

Molecular mechanism of lytic polysaccharide monooxygenases.

scientific article

Multireference Ab Initio Calculations on Reaction Intermediates of the Multicopper Oxidases

scientific article published on 01 December 2006

Multiscale Modelling of Lytic Polysaccharide Monooxygenases

scientific article published on 13 February 2017

Multiscale modeling of the active site of [Fe] hydrogenase: the H₂ binding site in open and closed protein conformations

scientific article published on 13 April 2015

NMR structure determination of proteins supplemented by quantum chemical calculations: detailed structure of the Ca2+ sites in the EGF34 fragment of protein S.

scientific article

Neutron structures of <i>Leishmania mexicana</i> triosephosphate isomerase in complex with reaction-intermediate mimics shed light on the proton-shuttling steps

scientific article published on 03 June 2021

Nonpolar Solvation Free Energies of Protein-Ligand Complexes

scientific article published on 28 September 2010

O2 Activation in Salicylate 1,2-Dioxygenase: A QM/MM Study Reveals the Role of His162.

scientific article published in November 2016

O2-binding to heme: electronic structure and spectrum of oxyheme, studied by multiconfigurational methods

scientific article published on 01 January 2005

On the Convergence of QM/MM Energies

scientific article published on 07 February 2011

On the Use of Interaction Entropy and Related Methods to Estimate Binding Entropies

scientific article published on 13 July 2021

On the role of the axial ligand in heme proteins: a theoretical study.

scientific article

On the significance of hydrogen bonds for the discrimination between CO and O2 by myoglobin

scientific article published on 01 February 1999

Performance of density functionals for first row transition metal systems

scientific article published on 01 January 2007

Predicting Relative Binding Affinity Using Nonequilibrium QM/MM Simulations

scientific article published on 08 November 2018

Prediction of activation energies for aromatic oxidation by cytochrome P450.

scientific article

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

scientific article published on 14 November 2011

Protein Influence on Electronic Spectra Modeled by Multipoles and Polarizabilities

scientific article published on 01 March 2009

Proton Transfer at Metal Sites in Proteins Studied by Quantum Mechanical Free-Energy Perturbations

scientific article published on 01 June 2008

Protonation States of Homocitrate and Nearby Residues in Nitrogenase Studied by Computational Methods and Quantum Refinement

scientific article published on 7 August 2017

Protonation and reduction of the FeMo cluster in nitrogenase studied by QM/MM calculations

article

Protonation states of intermediates in the reaction mechanism of [NiFe] hydrogenase studied by computational methods

scientific article published on 03 March 2016

QM/MM Calculations on Proteins.

scientific article published on 28 June 2016

QM/MM Study of the Catalytic Reaction of Myrosinase; Importance of Assigning Proper Protonation States of Active-Site Residues

scientific article published on 06 February 2021

QM/MM Study of the Conversion of Oxophlorin into Verdoheme by Heme Oxygenase.

scientific article published in November 2017

QM/MM study of the insertion of metal ion into protoporphyrin IX by ferrochelatase

scientific article published on 24 September 2009

QM/MM study of the reaction mechanism of sulfite oxidase.

scientific article published on 16 March 2018

QM/MM-PBSA method to estimate free energies for reactions in proteins.

scientific article published on 9 September 2008

Quantum Mechanics/Molecular Mechanics Study of the Reaction Mechanism of Glyoxalase I

scientific article published on 03 February 2020

Quantum Refinement Does Not Support Dinuclear Copper Sites in Crystal Structures of Particulate Methane Monooxygenase

scientific article published on 22 November 2017

Quantum chemistry can locally improve protein crystal structures.

scientific article published in November 2003

Quantum mechanical free energy barrier for an enzymatic reaction

scientific article published on 08 April 2005

Quantum refinement of [FeFe] hydrogenase indicates a dithiomethylamine ligand.

scientific article published in April 2010

Reaction Mechanism of [NiFe] Hydrogenase Studied by Computational Methods

scientific article published on 30 November 2018

Reaction mechanism of manganese superoxide dismutase studied by combined quantum and molecular mechanical calculations and multiconfigurational methods.

scientific article published in April 2009

Reaction mechanism of porphyrin metallation studied by theoretical methods.

scientific article published in February 2005

Redesign of the coenzyme specificity in L-lactate dehydrogenase from bacillus stearothermophilus using site-directed mutagenesis and media engineering

scientific article published on 01 October 1999

Reduction potentials and acidity constants of Mn superoxide dismutase calculated by QM/MM free-energy methods.

scientific article published on 29 September 2011

Reductive cleavage of the O-O bond in multicopper oxidases: a QM/MM and QM study

scientific article published on 01 January 2011

Relative Ligand-Binding Free Energies Calculated from Multiple Short QM/MM MD Simulations

scientific article published on 25 May 2018

Reorganization energy for internal electron transfer in multicopper oxidases

scientific article published on 19 October 2011

Restrained point-charge models for disaccharides.

scientific article published in February 2002

Secondary bonding interactions in biomimetic [2Fe-2S] clusters.

scientific article published on 8 February 2008

Simulation of the isotropic EXAFS spectra for the S2 and S3 structures of the oxygen evolving complex in photosystem II.

scientific article

Starting-Condition Dependence of Order Parameters Derived from Molecular Dynamics Simulations.

scientific article published on July 2010

Structural and photoluminescence properties of excited state intramolecular proton transfer capable compounds-potential emissive and electron transport materials

scientific article published on 01 June 2006

Structural insights into the active-ready form of [FeFe]-hydrogenase and mechanistic details of its inhibition by carbon monoxide

scientific article published on 04 August 2007

Structure and Energetics of Ligand-Fluorine Interactions with Galectin-3 Backbone and Side-Chain Amides: Insight into Solvation Effects and Multipolar Interactions

scientific article published on 11 July 2019

Structure of reduced and oxidized manganese superoxide dismutase: a combined computational and experimental approach

scientific article published on 01 June 2006

Structures of the high-valent metal-ion haem-oxygen intermediates in peroxidases, oxygenases and catalases.

scientific article

Substituted polyfluoroaryl interactions with an arginine side chain in galectin-3 are governed by steric-, desolvation and electronic conjugation effects

scientific article published on 01 January 2019

Sulfoxide, Sulfur, and Nitrogen Oxidation and Dealkylation by Cytochrome P450

scientific article published on 01 August 2008

Targeting intermediates of [FeFe]-hydrogenase by CO and CN vibrational signatures.

scientific article published on 28 March 2011

The Carbohydrate-Binding Site in Galectin-3 Is Preorganized To Recognize a Sugarlike Framework of Oxygens: Ultra-High-Resolution Structures and Water Dynamics

scientific article

The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities

scientific article

The coordination of the catalytic zinc in alcohol dehydrogenase studied by combined quantum-chemical and molecular mechanics calculations

scientific article published on 01 April 1996

The cupric geometry of blue copper proteins is not strained.

scientific article published in August 1996

The influence of axial ligands on the reduction potential of blue copper proteins.

scientific article published in October 1999

The neutron structure of urate oxidase resolves a long-standing mechanistic conundrum and reveals unexpected changes in protonation

scientific article

The normal-mode entropy in the MM/GBSA method: effect of system truncation, buffer region, and dielectric constant

scientific article published on 02 August 2012

The protonation status of compound II in myoglobin, studied by a combination of experimental data and quantum chemical calculations: quantum refinement.

scientific article

The reaction mechanism of iron and manganese superoxide dismutases studied by theoretical calculations

scientific article published on 01 September 2006

The structures of frataxin oligomers reveal the mechanism for the delivery and detoxification of iron.

scientific article published on October 2006

Theoretical 57Fe Mössbauer spectroscopy: isomer shifts of [Fe]-hydrogenase intermediates

scientific article published in 2014

Transition-State Docking of Flunitrazepam and Progesterone in Cytochrome P450.

scientific article

Two-Substrate Glyoxalase I Mechanism: A Quantum Mechanics/Molecular Mechanics Study

scientific article published on 14 December 2020

Understanding the Chemistry of Lead at a Molecular Level: The Pb(II) 6s6p Lone Pair Can Be Bisdirected in Proteins.

scientific article published on 23 April 2013

Unraveling the Reaction Mechanism of Mo/Cu CO Dehydrogenase Using QM/MM Calculations

scientific article published in 2022

Unraveling the similarity of the photoabsorption of deprotonated p-coumaric acid in the gas phase and within the photoactive yellow protein.

scientific article published on 6 December 2010

What Is the Structure of the E4 Intermediate in Nitrogenase?

scientific article published on 14 February 2020

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.

scientific article

Why does sulfite reductase employ siroheme?

scientific article published on 06 November 2019

Will molecular dynamics simulations of proteins ever reach equilibrium? ⬇️

scientific article published on May 22, 2012

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