U. Ryde

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

S. Genheden, U. Ryde, 2015, Expert opinion on drug discovery.

Molcas: a program package for computational chemistry.

B. Roos, P. Malmqvist, R. Lindh, 2003 .

Estimates of ligand-binding affinities supported by quantum mechanical methods

Jacob Kongsted, Samuel Genheden, Pär Söderhjelm, 2010, Interdisciplinary Sciences: Computational Life Sciences.

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

Francesco Aquilante, Pär Söderhjelm, Ulf Ryde, 2009, The journal of physical chemistry. B.

Ligand Affinities Estimated by Quantum Chemical Calculations.

Jacob Kongsted, Pär Söderhjelm, Ulf Ryde, 2010, Journal of chemical theory and computation.

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

Pär Söderhjelm, Ulf Ryde, U. Ryde, 2009, The journal of physical chemistry. A.

Performance of density functionals for first row transition metal systems.

Kasper P. Jensen, B. Roos, U. Ryde, 2007, The Journal of chemical physics.

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

M. Akke, S. Genheden, U. Ryde, 2009, Journal of biomolecular NMR.

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

U. Ryde, Pär Söderhjelm, A. Weis, 2006, Journal of medicinal chemistry.

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

U. Ryde, Pär Söderhjelm, 2016, Chemical reviews.

Quantum Mechanics in Structure‐Based Ligand Design

S. Genheden, U. Ryde, Pär Söderhjelm, 2012 .

Quantum chemistry can locally improve protein crystal structures.

Kristina Nilsson, Ulf Ryde, U. Ryde, 2003, Journal of the American Chemical Society.

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

Jacob Kongsted, Samuel Genheden, Pär Söderhjelm, 2011, Journal of the American Chemical Society.

Will molecular dynamics simulations of proteins ever reach equilibrium?

Samuel Genheden, Ulf Ryde, S. Genheden, 2012, Physical chemistry chemical physics : PCCP.

A combined quantum and molecular mechanical study of the O2 reductive cleavage in the catalytic cycle of multicopper oxidases.

Ulf Ryde, Lubomír Rulísek, U. Ryde, 2005, Inorganic chemistry.

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

U. Ryde, L. Cao, O. Caldararu, 2017, The journal of physical chemistry. B.

Theoretical studies of the active-site structure, spectroscopic and thermodynamic properties, and reaction mechanism of multicopper oxidases

U. Ryde, L. Rulíšek, 2013 .

Can the protonation state of histidine residues be determined from molecular dynamics simulations

Samuel Genheden, Paulius Mikulskis, Ulf Ryde, 2012 .

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

U. Ryde, L. Rulíšek, Martin Srnec, 2011, Chemphyschem : a European journal of chemical physics and physical chemistry.

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

Ulf Ryde, U. Ryde, M. Fuchs, 2009, JBIC Journal of Biological Inorganic Chemistry.

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

U. Ryde, Yaxue Wang, Yong Shen, 2009, Journal of inorganic biochemistry.

Protonation status of metal-bound ligands can be determined by quantum refinement.

Kristina Nilsson, Ulf Ryde, U. Ryde, 2004, Journal of inorganic biochemistry.

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

Samuel Genheden, Ulf Ryde, S. Genheden, 2011, Journal of chemical theory and computation.

Predicting Relative Binding Affinity Using Nonequilibrium QM/MM Simulations.

U. Ryde, Y. Mei, Meiting Wang, 2018, Journal of chemical theory and computation.

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

S. Genheden, U. Ryde, J. Uranga, 2017, J. Chem. Inf. Model..

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

Samuel Genheden, Paulius Mikulskis, Ulf Ryde, 2014, Journal of Molecular Modeling.

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

Samuel Genheden, Ulf Ryde, S. Genheden, 2012, Journal of chemical theory and computation.

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

Lars Olsen, Patrik Rydberg, Jacob Kongsted, 2008, Journal of chemical theory and computation.

QM/MM Calculations on Proteins.

U. Ryde, 2016, Methods in enzymology.

A Computational Comparison of Oxygen Atom Transfer Catalyzed by Dimethyl Sulfoxide Reductase with Mo and W

U. Ryde, R. Mata, Jilai Li, 2015 .

Theoretical study of the discrimination between O(2) and CO by myoglobin.

U. Ryde, E. Sigfridsson, Emma Sigfridsson, 2002, Journal of inorganic biochemistry.

Conformational Dependence of Isotropic Polarizabilities.

U. Ryde, J. Kongsted, Pär Söderhjelm, 2011, Journal of chemical theory and computation.

The axial N-base has minor influence on Co-C bond cleavage in cobalamins

Kasper P. Jensen, U. Ryde, 2002 .

Reorganization energy for internal electron transfer in multicopper oxidases.

Lihong Hu, S. Shleev, U. Ryde, 2011, The journal of physical chemistry. B.

Combined quantum and molecular mechanics calculations on metalloproteins.

Ulf Ryde, U. Ryde, 2003, Current opinion in chemical biology.

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

U. Ryde, T. Drakenberg, Y. Hsiao, 2005, Journal of biomolecular NMR.

The importance of porphyrin distortions for the ferrochelatase reaction

U. Ryde, E. Sigfridsson, Emma Sigfridsson, 2003, JBIC Journal of Biological Inorganic Chemistry.

On the role of covalent strain in protein function

U. Ryde, 2002 .

Automated orientation of water molecules in neutron crystallographic structures of proteins.

A. Eriksson, U. Ryde, E. Oksanen, 2020, Acta crystallographica. Section D, Structural biology.

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

U. Ryde, 2017, Journal of chemical theory and computation.

Multireference ab initio calculations on reaction intermediates of the multicopper oxidases.

Frank Neese, Ulf Ryde, Lubomír Rulísek, 2006, Inorganic chemistry.

Computational modelling of oxygenation processes in enzymes and biomimetic model complexes.

Matthew G. Quesne, P. Comba, U. Ryde, 2014, Chemical communications.

On the possibility of uphill intramolecular electron transfer in multicopper oxidases : electrochemical and quantum chemical study of bilirubin oxidase

S. Shleev, U. Ryde, C. Reimann, 2012 .

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

U. Ryde, L. De Gioia, M. Bruschi, 2010, Journal of the American Chemical Society.

Influence of the protein and DFT method on the broken‐symmetry and spin states in nitrogenase

U. Ryde, L. Cao, Lili Cao, 2018 .

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

Ulf Ryde, Lubomír Rulísek, U. Ryde, 2007, Journal of the American Chemical Society.

Quantum Crystallography: Current Developments and Future Perspectives.

C. F. Matta, M. Sierka, A. Madsen, 2018, Chemistry.

Multireference ab initio calculations of g tensors for trinuclear copper clusters in multicopper oxidases.

F. Neese, U. Ryde, E. Solomon, 2010, The journal of physical chemistry. B.

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

Martin A. Olsson, U. Ryde, Casper Steinmann, 2018, Journal of chemical theory and computation.

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

U. Ryde, J. Piquemal, O. Parisel, 2013, Journal of chemical theory and computation.

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

U. Ryde, S. Jafari, Nadia Kazemi, 2018, Inorganic chemistry.

Understanding the toxicology of lead at a molecular level: Pb(II) 6s lone pair can be bisdirected in proteins

U. Ryde, J. Piquemal, M. V. Severen, 2014 .

Multiscale Modelling of Lytic Polysaccharide Monooxygenases

U. Ryde, E. Hedegård, 2016, ACS omega.

Computationally enhanced X-ray diffraction analysis of a gold(III) complex interacting with the human telomeric DNA G-quadruplex. Unravelling non-unique ligand positioning.

U. Ryde, L. Messori, A. Nocentini, 2022, International journal of biological macromolecules.

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

U. Ryde, D. Logan, E. Oksanen, 2019, Physical chemistry chemical physics : PCCP.

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

G. Moro, U. Ryde, E. Sicilia, 2022, ACS Catalysis.

Rubus sordirosanthus in Halland, southwest Sweden

U. Ryde, G. Werlemark, 2010 .

On the Difference Between Additive and Subtractive QM/MM Calculations

U. Ryde, Lili Cao, 2018, Front. Chem..

N2H2 binding to the nitrogenase FeMo cluster studied by QM/MM methods

U. Ryde, Lili Cao, 2020, JBIC Journal of Biological Inorganic Chemistry.

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

U. Ryde, L. De Gioia, M. Bruschi, 2011, Chemistry.

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.

U. Ryde, L. De Gioia, M. Bruschi, 2009, Angewandte Chemie.

What Is the Structure of the E4 Intermediate in Nitrogenase?

U. Ryde, Lili Cao, 2020, Journal of chemical theory and computation.

Putative reaction mechanism of nitrogenase after dissociation of a sulfide ligand

U. Ryde, Lili Cao, 2020, Journal of Catalysis.

Does the crystal structure of vanadium nitrogenase contain a reaction intermediate? Evidence from quantum refinement

U. Ryde, O. Caldararu, Lili Cao, 2020, JBIC Journal of Biological Inorganic Chemistry.

Extremely large differences in DFT energies for nitrogenase models.

U. Ryde, Lili Cao, 2019, Physical chemistry chemical physics : PCCP.

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

U. Ryde, K. Pierloot, Q. Phung, 2017, Physical chemistry chemical physics : PCCP.

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

U. Ryde, L. Rulíšek, F. Aquilante, 2009, The journal of physical chemistry. B.

Computational Modelling of Oxygenation Processes in Enzymes and Biomimetic Model Complexes

P. Comba, U. Ryde, Bodo Martin, 2014 .

A comparison of the tetrapyrrole cofactors in nature and their tuning by axial ligands

Kasper P. Jensen, U. Ryde, J. Heimdal, 2008 .

Proceedings of the Chemical Society. June 1958

Matthew G. Quesne, P. Comba, U. Ryde, 1958 .

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

U. Ryde, G. Dong, 2016, Inorganic chemistry.

Mechanism of hydrogen peroxide formation by lytic polysaccharide monooxygenase† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c8sc03980a

U. Ryde, E. Oksanen, E. Hedegård, 2018, Chemical science.

Molecular mechanism of lytic polysaccharide monooxygenases

U. Ryde, E. Hedegård, 2018, Chemical science.

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

U. Ryde, P. Fantucci, L. Gioia, 2010 .

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

U. Ryde, M. Fuchs, F. Meyer, 2009, JBIC Journal of Biological Inorganic Chemistry.

Combined computational and crystallographic study of the oxidised states of [NiFe] hydrogenase

U. Ryde, Pär Söderhjelm, 2006 .

Protonation and Reduction of the FeMo Cluster in Nitrogenase Studied by Quantum Mechanics/Molecular Mechanics (QM/MM) Calculations.

U. Ryde, O. Caldararu, Lili Cao, 2018, Journal of chemical theory and computation.

Quantum refinement with multiple conformations: application to the P-cluster in nitrogenase

U. Ryde, Lili Cao, 2020, Acta crystallographica. Section D, Structural biology.

Water structure in solution and crystal molecular dynamics simulations compared to protein crystal structures

U. Ryde, E. Oksanen, O. Caldararu, 2020, RSC advances.

Molecular orbital theory.

B. Roos, U. Ryde, 2003 .

QM/MM Study of Partial Dissociation of S2B for the E2 Intermediate of Nitrogenase

U. Ryde, Hao Jiang, Oskar K G Svensson, 2022, Inorganic chemistry.

QM/MM study of the stereospecific proton exchange of glutathiohydroxyacetone by glyoxalase I

U. Ryde, S. Jafari, M. Irani, 2019, Results in Chemistry.

Why does sulfite reductase employ siroheme?

U. Ryde, R. Silaghi-Dumitrescu, Adrian M V Brânzanic, 2019, Chemical communications.

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

U. Ryde, A. Rosenzweig, O. Caldararu, 2018, Angewandte Chemie.

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

U. Ryde, J. Kongsted, O. Christiansen, 2011, Physical chemistry chemical physics : PCCP.

Metal ion enhanced binding of AMD3100 to Asp262 in the CXCR4 receptor.

Kasper P. Jensen, T. Schwartz, J. S. Jakobsen, 2003, Biochemistry.

Lactam hydrolysis catalyzed by mononuclear metallo-beta-lactamases: a density functional study

U. Ryde, L. Olsen, J. Antony, 2003 .

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

S. Genheden, U. Ryde, R. Hatti-Kaul, 2013, Biochemistry.

The Neutron Structure of Urate Oxidase Resolves a Long-Standing Mechanistic Conundrum and Reveals Unexpected Changes in Protonation

U. Ryde, E. Oksanen, M. Blakeley, 2014, PloS one.

QM/MM study of the conversion of biliverdin into verdoheme by heme oxygenase

Fatemeh S. Alavi, U. Ryde, N. Safari, 2019, Theoretical Chemistry Accounts.

Quantum Mechanical Calculations of Redox Potentials of the Metal Clusters in Nitrogenase

U. Ryde, Hao Jiang, Oskar K G Svensson, 2022, Molecules.

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

Martin A. Olsson, M. Akke, U. Ryde, 2019, Journal of the American Chemical Society.

Targeting the reactive intermediate in polysaccharide monooxygenases

U. Ryde, E. Hedegård, 2017, JBIC Journal of Biological Inorganic Chemistry.

The structure and function of blue copper proteins

U. Ryde, M. Olsson, K. Pierloot, 2001 .

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

U. Ryde, C. Schulzke, Kerstin Starke, 2009, JBIC Journal of Biological Inorganic Chemistry.

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

U. Ryde, Alexander Gaenko, A. Devarajan, 2006, The journal of physical chemistry. A.

Quantum refinement - a combination of quantum chemistry and protein crystallography.

Kristina Nilsson, Ulf Ryde, U. Ryde, 2003 .

Proteins, Blue Copper: Electronic Spectra

B. Roos, U. Ryde, M. Olsson, 2002 .

Structure, strain, and reorganization energy of blue copper models in the protein

Ulf Ryde, U. Ryde, M. Olsson, 2001 .

Quantum chemical calculations of the reorganization energy of blue‐copper proteins

U. Ryde, M. Olsson, U Ryde, 1998, Protein science : a publication of the Protein Society.

Protein strain in blue copper proteins studied by free energy perturbations

U. Ryde, Jan O.A. De Kerpel, U Ryde, 1999, Proteins.

Cobalamins uncovered by modern electronic structure calculations

Ulf Ryde, Kasper P. Jensen, U. Ryde, 2009 .

Relation between the Structure and Spectroscopic Properties of Blue Copper Proteins

Björn O. Roos, Ulf Ryde, B. Roos, 1998 .

The cupric geometry of blue copper proteins is not strained.

B. Roos, U. Ryde, M. Olsson, 1996, Journal of molecular biology.

On the role of strain in blue copper proteins

Björn O. Roos, Ulf Ryde, B. Roos, 2000, JBIC Journal of Biological Inorganic Chemistry.

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

U. Ryde, M. Olsson, U. Ryde, 1999, JBIC Journal of Biological Inorganic Chemistry.

On the relative stability of tetragonal and trigonal Cu(II) complexes with relevance to the blue copper proteins

B. Roos, U. Ryde, M. Olsson, 1998, JBIC Journal of Biological Inorganic Chemistry.

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

U. Ryde, L. Rulíšek, Jilai Li, 2015, The journal of physical chemistry. B.

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

U. Ryde, L. Rulíšek, 2006, The journal of physical chemistry. B.

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

U. Ryde, R. Mata, Jilai Li, 2013, Journal of chemical theory and computation.

QM/MM study of the reaction mechanism of sulfite oxidase

U. Ryde, R. Mata, E. Nordlander, 2018, Scientific Reports.

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

U. Ryde, R. Mata, M. V. Severen, 2014, JBIC Journal of Biological Inorganic Chemistry.

Effect of the protein ligand in DMSO reductase studied by computational methods.

U. Ryde, G. Dong, 2017, Journal of inorganic biochemistry.

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

U. Ryde, Jilai Li, 2014, Inorganic chemistry.

Quantum-refinement studies of the bidentate ligand of V‑nitrogenase and the protonation state of CO-inhibited Mo‑nitrogenase.

U. Ryde, E. Oksanen, J. Bergmann, 2021, Journal of inorganic biochemistry.

Refinement of protein structures using a combination of quantum-mechanical calculations with neutron and X-ray crystallographic data

U. Ryde, D. Logan, E. Oksanen, 2019, Acta crystallographica. Section D, Structural biology.

Accurate metal-site structures in proteins obtained by combining experimental data and quantum chemistry.

Ulf Ryde, U. Ryde, 2007, Dalton transactions.

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

Ulf Ryde, Lubomír Rulísek, Kasper P. Jensen, 2006, J. Comput. Chem..

Theoretical Insights into the Aerobic Hydrogenase Activity of Molybdenum–Copper CO Dehydrogenase

G. Moro, U. Ryde, M. Bruschi, 2019, Inorganics.

Interpretation of EXAFS spectra for sitting-atop complexes with the help of computational methods

Ulf Ryde, U. Ryde, Y. Hsiao, 2006 .

Reaction mechanism of porphyrin metallation studied by theoretical methods.

U. Ryde, Yong Shen, 2005, Chemistry.

The structure of sitting-atop complexes of metalloporphyrins studied by theoretical methods.

U. Ryde, Yong Shen, 2004, Journal of inorganic biochemistry.

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

U. Ryde, J. Kongsted, E. Hedegård, 2015, Angewandte Chemie.

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

Ulf Ryde, Piercarlo Fantucci, Claudio Greco, 2007, Inorganic chemistry.

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

U. Ryde, L. De Gioia, M. Bruschi, 2011, Inorganic chemistry.

Comparison of chemical properties of iron, cobalt, and nickel porphyrins, corrins, and hydrocorphins

Kasper P. Jensen, U. Ryde, 2005 .

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

U. Ryde, E. Bill, E. Bothe, 2008, Angewandte Chemie.

The coordination chemistry of the catalytic zinc ion in alcohol dehydrogenase studied by ab initio quantum chemical calculations

Ulf Ryde, U. Ryde, 1994 .

Theoretical prediction of the co-c bond strength in cobalamins.

Ulf Ryde, Kasper P. Jensen, U. Ryde, 2003 .

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

Ulf Ryde, U. Ryde, 1996, J. Comput. Aided Mol. Des..

A comparative reactivity study of microperoxidases based on hemin, mesohemin and deuterohemin.

U. Ryde, A. Barra, P. Rydberg, 2005, Journal of inorganic biochemistry.

Protein Flexibility and Conformational Entropy in Ligand Design Targeting the Carbohydrate Recognition Domain of Galectin-3

Olof Engström, Samuel Genheden, Ulf Ryde, 2010, Journal of the American Chemical Society.

How the Co-C bond is cleaved in coenzyme B12 enzymes: a theoretical study.

Ulf Ryde, Kasper P. Jensen, U. Ryde, 2005, Journal of the American Chemical Society.

Conversion of homocysteine to methionine by methionine synthase: a density functional study.

Kasper P. Jensen, U. Ryde, 2003, Journal of the American Chemical Society.

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

Kasper P. Jensen, U. Ryde, 2003, Chembiochem : a European journal of chemical biology.

Comparison of methods for deriving atomic charges from the electrostatic potential and moments

Ulf Ryde, Emma Sigfridsson, U. Ryde, 1998, J. Comput. Chem..

General Transition-State Force Field for Cytochrome P450 Hydroxylation.

Lars Olsen, Patrik Rydberg, Per-Ola Norrby, 2007, Journal of chemical theory and computation.

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

M. Akke, S. Genheden, U. Ryde, 2011, Biochemistry.

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

E. Garman, U. Ryde, S. Al-Karadaghi, 2006, Structure.

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

Patrik Rydberg, Ulf Ryde, Emma Sigfridsson, 2004, JBIC Journal of Biological Inorganic Chemistry.

Arguments for a narrow species concept in Rubus sect. Corylifolii

U. Ryde, 2011 .

Genetic analysis shows that Rubus vikensis is a distinct species with a disjunct distribution

U. Ryde, 2010 .

Quantum-mechanical studies of reactions performed by cytochrome P450 enzymes

Patrik Rydberg, Ulf Ryde, U. Ryde, 2012 .

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

Jacob Kongsted, Pär Söderhjelm, Ulf Ryde, 2009, J. Comput. Aided Mol. Des..

On the Convergence of QM/MM Energies.

Pär Söderhjelm, Ulf Ryde, LiHong Hu, 2011, Journal of chemical theory and computation.

The Normal-Mode Entropy in the MM/GBSA Method: Effect of System Truncation, Buffer Region, and Dielectric Constant

Daniel Hoffmann, Samuel Genheden, Paulius Mikulskis, 2012, J. Chem. Inf. Model..

Effect of covalent links on the structure, spectra, and redox properties of myeloperoxidase--a density functional study.

U. Ryde, Alexander Gaenko, A. Devarajan, 2008, Journal of inorganic biochemistry.

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

U. Ryde, R. Kaur, L. Hederstedt, 2009, Biopolymers.

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

Ulf Ryde, Jimmy Heimdal, LiHong Hu, 2009, The journal of physical chemistry. A.

A DFT investigation on structural and redox properties of a synthetic Fe6S6 assembly closely related to the [FeFe]-hydrogenases active site

U. Ryde, M. Bruschi, Giuseppe Zampella, 2008 .

Is density functional theory accurate for lytic polysaccharide monooxygenase enzymes?

U. Ryde, V. Veryazov, E. Hedegård, 2019, Dalton transactions.

Entropy–Entropy Compensation between the Protein, Ligand, and Solvent Degrees of Freedom Fine-Tunes Affinity in Ligand Binding to Galectin-3C

M. Akke, U. Ryde, D. Logan, 2021, JACS Au.

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

Pär Söderhjelm, Ulf Ryde, LiHong Hu, 2013, Journal of chemical theory and computation.

How to obtain statistically converged MM/GBSA results

Samuel Genheden, Ulf Ryde, S. Genheden, 2009, J. Comput. Chem..

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

U. Ryde, M. Hedrén, Melanie S Montes, 2022, Nordic Journal of Botany.

Hybrids between Rubus idaeus and Rubus sect. Corylifolii and their relation to R. pruinosus and R. rosanthus

U. Ryde, M. Hedrén, Mingyue Zhou, 2021, Nordic Journal of Botany.

Mechanistic and physiological implications of the interplay among iron-sulfur clusters in [FeFe]-hydrogenases. A QM/MM perspective.

U. Ryde, L. De Gioia, M. Bruschi, 2011, Journal of the American Chemical Society.

Magnetic Properties of [FeFe]-Hydrogenases: A Theoretical Investigation Based on Extended QM and QM/MM Models of the H-Cluster and Its Surroundings

U. Ryde, W. Lubitz, M. Bruschi, 2011 .

On the role of Glu‐68 in alcohol dehydrogenase

U. Ryde, U Ryde, Ulf Ryde, 1995, Protein science : a publication of the Protein Society.

Quantum Mechanical/Molecular Mechanical (QM/MM) Methods and Applictions in Bioinorganic Chemistry

U. Ryde, 2009 .

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

U. Ryde, T. Rod, K. Nilsson, 2004, Biophysical journal.

Quantum chemical geometry optimizations in proteins using crystallographic raw data

Kristina Nilsson, Lars Olsen, Ulf Ryde, 2002, J. Comput. Chem..

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

Francisco Adasme-Carreño, Ulf Ryde, Majda Misini Ignjatović, 2016, Journal of Computer-Aided Molecular Design.

How O2 Binds to Heme

Ulf Ryde, Kasper P. Jensen, U. Ryde, 2004, Journal of Biological Chemistry.

Comparison of force fields to study the zinc-finger containing protein NPL4, a target for Antabuse in cancer therapy

E. Papaleo, U. Ryde, M. Lambrughi, 2023, bioRxiv.

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

Ulf Ryde, LiHong Hu, Lihong Hu, 2011, Journal of chemical theory and computation.

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

Kristina Nilsson, Ulf Ryde, Emma Sigfridsson, 2003, Acta crystallographica. Section D, Biological crystallography.

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

U. Ryde, L. Bülow, N. Holmberg, 1999, Protein engineering.

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

Pär Söderhjelm, Ulf Ryde, Martin A. Olsson, 2016, J. Comput. Chem..

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

Ulf Ryde, Jimmy Heimdal, U. Ryde, 2012, Physical chemistry chemical physics : PCCP.

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

Lars Olsen, Patrik Rydberg, Samuel Genheden, 2012, Journal of Computer-Aided Molecular Design.

Reaction Mechanism of [NiFe] Hydrogenase Studied by Computational Methods.

U. Ryde, K. Pierloot, Q. Phung, 2018, Inorganic chemistry.

Carboxylate binding modes in zinc proteins: a theoretical study.

U. Ryde, U Ryde, 1999, Biophysical journal.

fragHAR: towards ab initio quantum-crystallographic X-ray structure refinement for polypeptides and proteins

U. Ryde, E. Oksanen, D. Jayatilaka, 2020, IUCrJ.

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

Geng Dong, Ulf Ryde, Erik D Hedegård, 2017, Physical chemistry chemical physics : PCCP.

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

U. Ryde, L. Rulíšek, Martin Srnec, 2011, Faraday discussions.

Protein Influence on Electronic Spectra Modeled by Multipoles and Polarizabilities.

Pär Söderhjelm, Massimo Olivucci, Ulf Ryde, 2009, Journal of chemical theory and computation.

How are hydrogen bonds modified by metal binding?

U. Ryde, Charlotte Husberg, 2013, JBIC Journal of Biological Inorganic Chemistry.

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.

U. Ryde, L. De Gioia, M. Bruschi, 2011, Chemphyschem : a European journal of chemical physics and physical chemistry.

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

Ulf Ryde, Kasper P. Jensen, B. Roos, 2005, Journal of inorganic biochemistry.

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

Pär Söderhjelm, Ulf Ryde, Jimmy Heimdal, 2008, Journal of chemical theory and computation.

Comparison of the accuracy of DFT methods for reactions with relevance to nitrogenase

U. Ryde, Magne Torbjörnsson, 2021, Electronic Structure.

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

U. Ryde, A. Fouda, 2016, Journal of chemical theory and computation.

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

Mickaël G. Delcey, R. Lindh, U. Ryde, 2014, Physical chemistry chemical physics : PCCP.

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

Stefan Grimme, Ulf Ryde, Ricardo A Mata, 2011, Dalton transactions.

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

U. Ryde, Yuxiang Bu, Xiaoli Sun, 2014, The journal of physical chemistry. B.

Theoretical study of the electronic spectrum of plastocyanin

B. Roos, U. Ryde, K. Pierloot, 1997 .

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

Emma Sigfridsson, U. Ryde, U. Ryde, 1999, JBIC Journal of Biological Inorganic Chemistry.

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

Ulf Ryde, Ulf J. Nilsson, U. Ryde, 2019, ChemMedChem.

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

U. Ryde, D. Logan, U. Nilsson, 2019, Organic & biomolecular chemistry.

Exploring ligand dynamics in protein crystal structures with ensemble refinement

U. Ryde, D. Logan, E. Oksanen, 2021, Acta crystallographica. Section D, Structural biology.

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

U. Ryde, Vilhelm Ekberg, 2021, Journal of chemical theory and computation.

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

Samuel Genheden, Ulf Ryde, Mikael Akke, 2014, Journal of chemical theory and computation.

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

Samuel Genheden, Ulf Ryde, S. Genheden, 2011, J. Comput. Chem..

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

Samuel Genheden, Ulf Ryde, Mikael Akke, 2010, Journal of chemical theory and computation.

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

U. Ryde, R. Wierenga, N. Coquelle, 2021, IUCrJ.

Refinement of protein structures using a combination of quantum-mechanical calculations with neutron and X-ray crystallographic data. Corrigendum

U. Ryde, D. Logan, E. Oksanen, 2020, Acta crystallographica. Section D, Structural biology.

Correction: Mechanism of hydrogen peroxide formation by lytic polysaccharide monooxygenase

U. Ryde, E. Oksanen, E. Hedegård, 2019, Chemical Science.

Molecular mechanism of lytic polysaccharide monooxygenases

U. Ryde, E. Hedegård, 2018 .

Galectin-3C in complex with substituted fluoroaryltriazole monothiogalactoside derivative 1

U. Ryde, D. Logan, U. Nilsson, 2019 .

Molecular dynamics simulations of alcohol dehydrogenase with a four‐ or five‐coordinate catalytic zinc ion

U. Ryde, U Ryde, 1995, Proteins.

Comparison of Grand Canonical and Conventional Molecular Dynamics Simulation Methods for Protein-Bound Water Networks

Marley L. Samways, J. Essex, U. Ryde, 2022, ACS Physical Chemistry Au.

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

Andriy Kovalenko, Samuel Genheden, Ulf Ryde, 2010, The journal of physical chemistry. B.

Insight into the reaction mechanism of lipoyl synthase: a QM/MM study

U. Ryde, G. Dong, Lili Cao, 2017, JBIC Journal of Biological Inorganic Chemistry.

Restrained point‐charge models for disaccharides

Bruce L. Bush, Ulf Ryde, Emma Sigfridsson, 2002, J. Comput. Chem..

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

U. Ryde, S. Jafari, M. Irani, 2022, Inorganic chemistry.

A Large-Scale Test of Free-Energy Simulation Estimates of Protein-Ligand Binding Affinities

Samuel Genheden, Paulius Mikulskis, Ulf Ryde, 2014, J. Chem. Inf. Model..

A fundamental view of enthalpy–entropy compensation

U. Ryde, 2014 .

Comparison of MM/GBSA calculations based on explicit and implicit solvent simulations.

Samuel Genheden, Pär Söderhjelm, Ulf Ryde, 2013, Physical chemistry chemical physics : PCCP.

The role of axial ligands for the structure and function of chlorophylls

Kasper P. Jensen, U. Ryde, J. Heimdal, 2006, JBIC Journal of Biological Inorganic Chemistry.

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

Pär Söderhjelm, Ulf Ryde, U. Ryde, 2013, Journal of chemical theory and computation.

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

U. Ryde, L. De Gioia, M. Bruschi, 2007, Inorganic chemistry.

Metal binding to Bacillus subtilis ferrochelatase and interaction between metal sites

U. Ryde, S. Al-Karadaghi, U. Olsson, 2003, JBIC Journal of Biological Inorganic Chemistry.

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

U. Ryde, J. Bergmann, Lili Cao, 2019, Inorganic chemistry.

QM/MM study of the binding of H2 to MoCu CO dehydrogenase: development and applications of improved H2 van der Waals parameters

U. Ryde, C. Greco, Anna Rovaletti, 2021, Journal of Molecular Modeling.

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

Ulf Ryde, Claudio Greco, U. Ryde, 2010, Journal of the American Chemical Society.

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

U. Ryde, P. Rydberg, C. Görbitz, 2006, Journal of inorganic biochemistry.

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

Ulf Ryde, Per E M Siegbahn, Xichen Li, 2015, Proceedings of the National Academy of Sciences.

Multireference Protonation Energetics of a Dimeric Model of Nitrogenase Iron–Sulfur Clusters

Seunghoon Lee, G. Chan, U. Ryde, 2023, The journal of physical chemistry. A.

Proton Transfer Pathways in Nitrogenase with and without Dissociated S2B

U. Ryde, Hao Jiang, Lili Cao, 2022, Angewandte Chemie.

Thermodynamically Favourable States in the Reaction of Nitrogenase without Dissociation of any Sulfide Ligand

U. Ryde, Hao Jiang, 2022, Chemistry.

Critical evaluation of a crystal structure of nitrogenase with bound N2 ligands

U. Ryde, E. Oksanen, J. Bergmann, 2021, JBIC Journal of Biological Inorganic Chemistry.

Accuracy of typical approximations in classical models of intermolecular polarization.

Pär Söderhjelm, Ulf Ryde, Gunnar Karlström, 2008, The Journal of chemical physics.

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

Roland Lindh, Pär Söderhjelm, Ulf Ryde, 2007, J. Comput. Chem..

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

U. Ryde, G. Karlström, Pär Söderhjelm, 2006, The Journal of chemical physics.

Prediction of activation energies for aromatic oxidation by cytochrome P450.

Lars Olsen, Patrik Rydberg, Ulf Ryde, 2008, The journal of physical chemistry. A.

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

U. Ryde, S. Jafari, M. Irani, 2021, Journal of chemical theory and computation.

A comparison of the inner-sphere reorganization energies of cytochromes, iron-sulphur clusters, and blue copper proteins

Ulf Ryde, Emma Sigfridsson, U. Ryde, 2001 .

Inner-sphere reorganization energy of iron-sulfur clusters studied with theoretical methods.

U. Ryde, M. Olsson, U Ryde, 2001, Inorganic chemistry.

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

Samuel Genheden, Pär Söderhjelm, Ulf Ryde, 2015, J. Comput. Chem..

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

U. Ryde, G. Dong, 2016, JBIC Journal of Biological Inorganic Chemistry.

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

Jacob Kongsted, Ulf Ryde, Stefan Knecht, 2014, Physical chemistry chemical physics : PCCP.

The Influence of X‐Rays on the Structural Studies of Peroxide‐Derived Myoglobin Intermediates

U. Ryde, Y. Hsiao, C. Görbitz, 2008, Chemistry & biodiversity.

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

Fatemeh S. Alavi, U. Ryde, N. Safari, 2018, Dalton transactions.

Dynamics of water molecules in the active-site cavity of human cytochromes P450.

Lars Olsen, Patrik Rydberg, Ulf Ryde, 2007, The journal of physical chemistry. B.

Theoretical EXAFS studies of a model of the oxygen-evolving complex of photosystem II obtained with the quantum cluster approach

Guangju Chen, Ulf Ryde, Eduardo M. Sproviero, 2013 .

Catalytic Reaction Mechanism of Glyoxalase II: A Quantum Mechanics/Molecular Mechanics Study.

U. Ryde, S. Jafari, M. Irani, 2023, The journal of physical chemistry. B.

Histidine oxidation in lytic polysaccharide monooxygenase

U. Ryde, E. Hedegård, Magne Torbjörnsson, 2023, JBIC Journal of Biological Inorganic Chemistry.

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

Pär Söderhjelm, Ulf Ryde, Ricardo A Mata, 2014, Chemphyschem : a European journal of chemical physics and physical chemistry.

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

Ricardo A. Mata, Samuel Genheden, Pär Söderhjelm, 2014, Journal of Computer-Aided Molecular Design.

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

Lars Olsen, Patrik Rydberg, Ulf Ryde, 2008, Journal of chemical theory and computation.

The crystal structure of peroxymyoglobin generated through cryoradiolytic reduction of myoglobin compound III during data collection.

U. Ryde, Y. Hsiao, C. Görbitz, 2008, The Biochemical journal.

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

Samuel Genheden, Ulf Ryde, S. Genheden, 2012, Proteins.

Geometry, reduction potential, and reorganization energy of the binuclear Cu(A) site, studied by density functional theory.

U. Ryde, M. Olsson, U Ryde, 2001, Journal of the American Chemical Society.

QM/MM study of the reaction mechanism of sulfite oxidase

U. Ryde, R. Mata, E. Nordlander, 2018, Scientific Reports.

N2 binding to the E0-E4 states of nitrogenase.

Hao Jiang, U. Ryde, 2023, Dalton transactions.

EXAFS structure refinement supplemented by computational chemistry

Ulf Ryde, U. Ryde, R. A. Scott, 2006 .

A semiempirical approach to ligand‐binding affinities: Dependence on the Hamiltonian and corrections

Samuel Genheden, Paulius Mikulskis, Ulf Ryde, 2012, J. Comput. Chem..

On the significance of the trigger reaction in the action of the calicheamicin γ1I anti-cancer drug

R. Lindh, M. Schütz, U. Ryde, 1997 .

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

Samuel Genheden, Ulf Ryde, Antonella Ciancetta, 2011, J. Comput. Aided Mol. Des..

drogen peroxide formation by lytic polysaccharide monooxygenase †

U. Ryde, E. Oksanen, E. Hedegård, 2018 .

A theoretical study of the copper–cysteine bond in blue copper proteins

Björn O. Roos, Ulf Ryde, Antonio Carlos Borin, 2001 .

Theoretical Study of the Structural and Spectroscopic Properties of Stellacyanin

B. Roos, U. Ryde, K. Pierloot, 1998 .

Prediction and rationalization of the pH dependence of the activity and stability of family 11 xylanases.

Jan H. Jensen, Jacob Kongsted, Ulf Ryde, 2007, Biochemistry.

A thiocarbonate sink on the enzymatic energy landscape of aerobic CO oxidation? Answers from DFT and QM/MM models of Mo Cu CO-dehydrogenases

G. Moro, U. Ryde, M. Bruschi, 2019, Journal of Catalysis.

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

Patrik Rydberg, Ulf Ryde, U. Ryde, 2006, The Journal of chemical physics.

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

Ulf Ryde, Francesco Manzoni, U. Ryde, 2018, Journal of Computer-Aided Molecular Design.

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

Fatemeh S. Alavi, U. Ryde, N. Safari, 2017, The journal of physical chemistry. B.

Transferability of conformational dependent charges from protein simulations

Samuel Genheden, Pär Söderhjelm, Ulf Ryde, 2012 .

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

Jacob Kongsted, Ulf Ryde, U. Ryde, 2009, J. Comput. Aided Mol. Des..

Catalytic mechanism of human glyoxalase i studied by quantum-mechanical cluster calculations

U. Ryde, S. Jafari, M. Irani, 2016 .

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

Ulf Ryde, Martin A. Olsson, U. Ryde, 2017, Journal of chemical theory and computation.

Conformational dependence of charges in protein simulations

Pär Söderhjelm, Ulf Ryde, U. Ryde, 2009, J. Comput. Chem..

Reaction mechanism of formate dehydrogenase studied by computational methods

U. Ryde, G. Dong, 2018, JBIC Journal of Biological Inorganic Chemistry.

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

Frank Neese, Ulf Ryde, Martin A. Olsson, 2016, Journal of Computer-Aided Molecular Design.

Nonpolar Solvation Free Energies of Protein-Ligand Complexes.

Jacob Kongsted, Samuel Genheden, Pär Söderhjelm, 2010, Journal of chemical theory and computation.

Supporting Information Mechanism of hydrogen peroxide formation by lytic polysaccharide monooxygenase

U. Ryde, E. Oksanen, E. Hedegård, 2019 .

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

Ulf Ryde, U. Ryde, T. Rod, 2005, Journal of chemical theory and computation.

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

U. Ryde, A. Rosenzweig, Lili Cao, 2018, Angewandte Chemie.

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

U. Ryde, E. Hedegård, Hans Jørgen Aa Jensen, 2017, Physical chemistry chemical physics : PCCP.

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

S. Genheden, U. Ryde, 2012, Proteins: Structure, Function, and Bioinformatics.

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

Lihong Hu, S. Genheden, U. Ryde, 2011, Journal of the American Chemical Society.

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

M. Akke, S. Genheden, U. Ryde, 2009, Journal of biomolecular NMR.

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

Pär Söderhjelm, Paulius Mikulskis, Ulf Ryde, 2018, J. Comput. Chem..

The Normal-Mode Entropy in the MM/GBSA Method: Effect of System Truncation, Buffer Region, and Dielectric Constant

S. Genheden, U. Ryde, D. Hoffmann, 2012, J. Chem. Inf. Model..

Binding Affinities of Factor Xa Inhibitors Estimated by Thermodynamic Integration and MM/GBSA

Samuel Genheden, Ingemar Nilsson, Ulf Ryde, 2011, J. Chem. Inf. Model..

Ligand Affinities Estimated by Quantum Chemical Calculations.

U. Ryde, J. Kongsted, Pär Söderhjelm, 2010, Journal of chemical theory and computation.

Conformational dependence of charges in protein simulations

U. Ryde, Pär Söderhjelm, 2009, J. Comput. Chem..

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

U. Ryde, Lili Cao, Octav Caldararu, 2017, The journal of physical chemistry. B.

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

U. Ryde, L. Rulíšek, Jilai Li, 2015, Journal of Physical Chemistry B.

On the Convergence of QM/MM Energies.

Lihong Hu, U. Ryde, Pär Söderhjelm, 2011, Journal of chemical theory and computation.

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

U. Ryde, Pär Söderhjelm, J. Heimdal, 2008, The journal of physical chemistry. B.

Quantum mechanical free energy barrier for an enzymatic reaction.

Ulf Ryde, U. Ryde, T. Rod, 2005, Physical review letters.

Two local minima for structures of [4Fe–4S] clusters obtained with density functional theory methods

U. Ryde, S. Jafari, M. Irani, 2023, Scientific reports.

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

Fatemeh S. Alavi, U. Ryde, A. Fouda, 2020, Inorganic chemistry.

Reaction mechanism of formate dehydrogenase studied by computational methods

U. Ryde, G. Dong, 2018, JBIC Journal of Biological Inorganic Chemistry.

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

Fatemeh S. Alavi, U. Ryde, N. Safari, 2018, Dalton transactions.

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

Alfonso T. García-Sosa, Ulf Ryde, Martin A. Olsson, 2017, Journal of Computer-Aided Molecular Design.

Erratum to “O2-binding to heme: electronic structure and spectrum of oxyheme, studied by multiconfigurational methods” [J. Inorg. Biochem. 99(1) (2004) 45–54]

Björn O. Roos, Ulf Ryde, Kasper P. Jensen, 2005 .

The coordination chemistry of the structural zinc ion in alcohol dehydrogenase studied by ab initio quantum chemical calculations

Ulf Ryde, U. Ryde, 1996, European Biophysics Journal.

Molecular dynamic simulations of alcohol dehydrogenase with a four-or five-coordinate catalytic zinc ion by Ulf Ryde

U. Ryde, 2017 .

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

S. Genheden, U. Ryde, Pär Söderhjelm, 2015, J. Comput. Chem..

Assessment of DFT functionals for a minimal nitrogenase [Fe(SH)4H]- model employing state-of-the-art ab initio methods.

Seunghoon Lee, G. Chan, U. Ryde, 2023, The Journal of chemical physics.

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

U. Ryde, J. Kongsted, S. Knecht, 2014, Physical chemistry chemical physics : PCCP.

Protonation of Homocitrate and the E1 State of Fe-Nitrogenase Studied by QM/MM Calculations

U. Ryde, Hao Jiang, Kristoffer J M Lundgren, 2023, Inorganic chemistry.

Protein Influence on Electronic Spectra Modeled by Multipoles and Polarizabilities.

U. Ryde, M. Olivucci, Pär Söderhjelm, 2009, Journal of chemical theory and computation.

Importance of the iron-sulfur component and of the siroheme modification in the resting state of sulfite reductase.

U. Ryde, Adrian M. V. Brânzanic, Radu Silaghi-Dumitrescu, 2019, Journal of inorganic biochemistry.

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

U. Ryde, Yuxiang Bu, Xiaoli Sun, 2014, The journal of physical chemistry. B.

Prediction of activation energies for hydrogen abstraction by cytochrome p450.

Lars Olsen, Patrik Rydberg, Ulf Ryde, 2006, Journal of medicinal chemistry.