Ulf Ryde
Professor
Research areas
- Biochemical molecules studied by theoretical methods.
- The relation between structure and function of proteins.
- Enzyme mechanisms.
- The influence of the protein on bound metals, ligands and chromophores.
- Nature’s design of proteins (Why was that metal or amino acid selected?).
- QM/MM methods.
- Combination of QM methods and experimental methods: e.g. X-ray crystallography, NMR, EXAFS, neutron crystallography.
- Ligand binding.
Links
Links will open on Ulf’s personal website:
Publications
Displaying of publications. Sorted by year, then title.
Impact of Varying Velocities and Solvation Boxes on Alchemical Free-Energy Simulations
Meiting Wang, Hao Jiang, Ulf Ryde
(2025) Journal of Chemical Information and Modeling
Journal articleThe CuB site in particulate methane monooxygenase may be used to produce hydrogen peroxide
Kristoffer J.M. Lundgren, Lili Cao, Magne Torbjörnsson, Erik D. Hedegård, Ulf Ryde
(2025) Dalton Transactions, 54 p.3141-3156
Journal articleInvestigating the Substrate Oxidation Mechanism in Lytic Polysaccharide Monooxygenase : H2O2- versus O2-Activation
Marlisa M. Hagemann, Erna K. Wieduwilt, Ulf Ryde, Erik D. Hedegård
(2024) Inorganic Chemistry, 63 p.21929-21940
Journal articleQuantum refinement in real and reciprocal space using the Phenix and ORCA software
Kristoffer J.M. Lundgren, Octav Caldararu, Esko Oksanen, Ulf Ryde
(2024) IUCrJ, 11 p.921-937
Journal articleRubus wahlbergii and related species in Sweden
Mingyue Zhou, Melanie S. Montes, Tore Mattsson, Tomas Burén, Mikael Hedrén, et al.
(2024) Nordic Journal of Botany, 2024
Journal articleReaction Mechanism for CO Reduction by Mo-Nitrogenase Studied by QM/MM
Hao Jiang, Ulf Ryde
(2024) Inorganic Chemistry, 63 p.15951-15963
Journal articleCO Oxidation Mechanism of Silver-Substituted Mo/Cu CO-Dehydrogenase – Analogies and Differences to the Native Enzyme
Anna Rovaletti, Giorgio Moro, Ugo Cosentino, Ulf Ryde, Claudio Greco
(2024) ChemPhysChem, 25
Journal articlePutative reaction mechanism of nitrogenase with a half-dissociated S2B ligand
Hao Jiang, Ulf Ryde
(2024) Dalton Transactions, 53 p.11500-11513
Journal articleUnraveling the Binding Mode of Cyclic Adenosine–Inosine Monophosphate (cAIMP) to STING through Molecular Dynamics Simulations
Meiting Wang, Baoyi Fan, Wenfeng Lu, Ulf Ryde, Yuxiao Chang, et al.
(2024) Molecules, 29
Journal articleInterplay of halogen bonding and solvation in protein-ligand binding
Maria Luisa Verteramo, Majda Misini Ignjatović, Rohit Kumar, Sven Wernersson, Vilhelm Ekberg, et al.
(2024) iScience, 27
Journal articleQM/MM study of the catalytic reaction of aphid myrosinase
Sonia Jafari, Ulf Ryde, Mehdi Irani
(2024) International Journal of Biological Macromolecules, 262
Journal articleScalar Relativistic All-Electron and Pseudopotential Ab Initio Study of a Minimal Nitrogenase [Fe(SH)4H]− Model Employing Coupled-Cluster and Auxiliary-Field Quantum Monte Carlo Many-Body Methods
Victor P. Vysotskiy, Claudia Filippi, Ulf Ryde
(2024) Journal of Physical Chemistry A, 128 p.1358-1374
Journal articleConvergence criteria for single-step free-energy calculations : the relation between the Π bias measure and the sample variance
Meiting Wang, Ye Mei, Ulf Ryde
(2024) Chemical Science, 15 p.8786-8799
Journal articleH2 formation from the E2–E4 states of nitrogenase
Hao Jiang, Ulf Ryde
(2024) Physical Chemistry Chemical Physics, 26 p.1364-1375
Journal articleProtonation of Homocitrate and the E1 State of Fe-Nitrogenase Studied by QM/MM Calculations
Hao Jiang, Kristoffer j. m. Lundgren, Ulf Ryde
(2023) Inorganic Chemistry, 62 p.19433-19445
Journal articleAssessment of DFT functionals for a minimal nitrogenase [Fe(SH)4H]− model employing state-of-the-art ab initio methods
Victor P. Vysotskiy, Magne Torbjörnsson, Hao Jiang, Dennis Larsson, Lili Cao, et al.
(2023) The Journal of chemical physics, 159
Journal articleN2 binding to the E0–E4 states of nitrogenase
Hao Jiang, Ulf Ryde
(2023) Dalton Transactions, 52 p.9104-9120
Journal article(2963) Proposal to reject the name Rubus pseudoidaeus (Rosaceae)
Abraham van de Beek, Detlev Drenckhahn, Hendrik DeVriese, Thomas Gregor, Erik van den Ham, et al.
(2023) Taxon, 72 p.672-673
Journal article (comment)Catalytic Reaction Mechanism of Glyoxalase II : A Quantum Mechanics/Molecular Mechanics Study
Javad Shirazi, Sonia Jafari, Ulf Ryde, Mehdi Irani
(2023) Journal of Physical Chemistry B, 127 p.4480-4495
Journal articleHistidine oxidation in lytic polysaccharide monooxygenase
Magne Torbjörnsson, Marlisa M. Hagemann, Ulf Ryde, Erik Donovan Hedegård
(2023) Journal of Biological Inorganic Chemistry, 28 p.317-328
Journal articleTwo local minima for structures of [4Fe–4S] clusters obtained with density functional theory methods
Sonia Jafari, Ulf Ryde, Mehdi Irani
(2023) Scientific Reports, 13
Journal articleComparison of force fields to study the zinc-finger containing protein NPL4, a target for disulfiram in cancer therapy
Simone Scrima, Matteo Tiberti, Ulf Ryde, Matteo Lambrughi, Elena Papaleo
(2023) Biochimica et Biophysica Acta - Proteins and Proteomics, 1871
Journal articleQuantum Mechanical Calculations of Redox Potentials of the Metal Clusters in Nitrogenase
Hao Jiang, Oskar K. G. Svensson, Ulf Ryde
(2023) Molecules, 28
Journal articleA computational study of the reaction mechanism and stereospecificity of dihydropyrimidinase
Wijitra Meelua, Tanchanok Wanjai, Natechanok Thinkumrob, Julianna Oláh, James R.Ketudat Cairns, et al.
(2023) Physical Chemistry Chemical Physics, 25 p.8767-8778
Journal articleMultireference Protonation Energetics of a Dimeric Model of Nitrogenase Iron-Sulfur Clusters
Huanchen Zhai, Seunghoon Lee, Zhi Hao Cui, Lili Cao, Ulf Ryde, et al.
(2023) Journal of Physical Chemistry A, 127 p.9974-9984
Journal articleHow 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
Anna Rovaletti, Ulf Ryde, Giorgio Moro, Ugo Cosentino, Claudio Greco
(2022) Physical chemistry chemical physics : PCCP, 24 p.29471-29479
Journal articleHybrids between Rubus caesius and Rubus sect. Corylifolii (Rosaceae) and their relation to R. cyclomorphus, R. tiliaster, R. glauciformis, R. slesvicensis and R. firmus
Marcus Lewin, Mingyue Zhou, Melanie S. Montes, Tore Mattsson, Tomas Burén, et al.
(2022) Nordic Journal of Botany, 2022
Journal articleQM/MM Study of Partial Dissociation of S2B for the E2 Intermediate of Nitrogenase
Hao Jiang, Oskar K. G. Svensson, Ulf Ryde
(2022) Inorganic Chemistry, 61 p.18067-18076
Journal articleProton Transfer Pathways in Nitrogenase with and without Dissociated S2B
Hao Jiang, Oskar K. G. Svensson, Lili Cao, Ulf Ryde
(2022) Angewandte Chemie (International edition), 61
Journal articleComputationally enhanced X-ray diffraction analysis of a gold(III) complex interacting with the human telomeric DNA G-quadruplex. Unravelling non-unique ligand positioning
Damiano Cirri, Carla Bazzicalupi, Ulf Ryde, Justin Bergmann, Francesca Binacchi, et al.
(2022) International Journal of Biological Macromolecules, 211 p.506-513
Journal articleUnraveling the Reaction Mechanism of Mo/Cu CO Dehydrogenase Using QM/MM Calculations
Alessandra G. Ritacca, Anna Rovaletti, Giorgio Moro, Ugo Cosentino, Ulf Ryde, et al.
(2022) ACS Catalysis, 12 p.7336-7343
Journal articleThermodynamically Favourable States in the Reaction of Nitrogenase without Dissociation of any Sulfide Ligand
Hao Jiang, Ulf Ryde
(2022) Chemistry - A European Journal, 28
Journal articleCan Water Act as a Nucleophile in CO Oxidation Catalysed by Mo/Cu CO-Dehydrogenase? Answers from Theory
Anna Rovaletti, Giorgio Moro, Ugo Cosentino, Ulf Ryde, Claudio Greco
(2022) ChemPhysChem, 23
Journal articleCombining crystallography with quantum mechanics
Justin Bergmann, Esko Oksanen, Ulf Ryde
(2022) Current Opinion in Structural Biology, 72 p.18-26
Journal article reviewBenchmark Study of Redox Potential Calculations for Iron-Sulfur Clusters in Proteins
Sonia Jafari, Yakini A. Tavares Santos, Justin Bergmann, Mehdi Irani, Ulf Ryde
(2022) Inorganic Chemistry, 61 p.5991-6007
Journal articleComparison of Grand Canonical and Conventional Molecular Dynamics Simulation Methods for Protein-Bound Water Networks
Vilhelm Ekberg, Marley L. Samways, Majda Misini Ignjatović, Jonathan W. Essex, Ulf Ryde
(2022) ACS Physical Chemistry Au, 2 p.247-259
Journal articleCan the results of quantum refinement be improved with a continuum-solvation model?
Justin Bergmann, Esko Oksanen, Ulf Ryde
(2021) Acta Crystallographica. Section B: Structural Science, 77 p.906-918
Journal articleComparison of the accuracy of DFT methods for reactions with relevance to nitrogenase
Magne Torbjörnsson, Ulf Ryde
(2021) Electronic Structure, 3
Journal articleHybrids between Rubus idaeus and Rubus sect. Corylifolii and their relation to R. pruinosus and R. rosanthus
Ulf Ryde, Melanie S. Montes, Mingyue Zhou, Tore Mattsson, Tomas Burén, et al.
(2021) Nordic Journal of Botany, 39
Journal articleOn the Use of Interaction Entropy and Related Methods to Estimate Binding Entropies
Vilhelm Ekberg, Ulf Ryde
(2021) Journal of Chemical Theory and Computation, 17 p.5379-5391
Journal articleNeutron structures of Leishmania mexicana triosephosphate isomerase in complex with reaction-intermediate mimics shed light on the proton-shuttling steps
Vinardas Kelpšas, Octav Caldararu, Matthew P. Blakeley, Nicolas Coquelle, Rikkert K. Wierenga, et al.
(2021) IUCrJ, 8 p.633-643
Journal articleCritical evaluation of a crystal structure of nitrogenase with bound N2 ligands
Justin Bergmann, Esko Oksanen, Ulf Ryde
(2021) Journal of Biological Inorganic Chemistry, 26 p.341-353
Journal articleNorske bjørnebær 6. Sørlandsbjørnebær Rubus ”firmus”
Kåre Arnstein Lye, Ulf Ryde
(2021) Blyttia: norsk botanisk forenings tidsskrift, 79 p.39-45
Journal articleQM/MM Study of the Catalytic Reaction of Myrosinase; Importance of Assigning Proper Protonation States of Active-Site Residues
Sonia Jafari, Ulf Ryde, Mehdi Irani
(2021) Journal of Chemical Theory and Computation, 17 p.1822-1841
Journal articleEntropy–Entropy Compensation between the Protein, Ligand, and Solvent Degrees of Freedom Fine-Tunes Affinity in Ligand Binding to Galectin-3C
Johan Wallerstein, Vilhelm Ekberg, Majda Misini Ignjatović, Rohit Kumar, Octav Caldararu, et al.
(2021) Journal of the American Chemical Society, 1 p.484-500
Journal articleQM/MM study of the binding of H2 to MoCu CO dehydrogenase : development and applications of improved H2 van der Waals parameters
Anna Rovaletti, Claudio Greco, Ulf Ryde
(2021) Journal of Molecular Modeling, 27
Journal articleQuantum-refinement studies of the bidentate ligand of V‑nitrogenase and the protonation state of CO-inhibited Mo‑nitrogenase
Justin Bergmann, Esko Oksanen, Ulf Ryde
(2021) Journal of Inorganic Biochemistry, 219
Journal articleTwo-Substrate Glyoxalase i Mechanism : A Quantum Mechanics/Molecular Mechanics Study
Sonia Jafari, Ulf Ryde, Mehdi Irani
(2021) Inorganic Chemistry , p.303-314
Journal articleExploring ligand dynamics in protein crystal structures with ensemble refinement
Octav Caldararu, Vilhelm Ekberg, Derek T. Logan, Esko Oksanen, Ulf Ryde
(2021) Acta Crystallographica Section D: Structural Biology, 77 p.1099-1115
Journal articlePutative reaction mechanism of nitrogenase after dissociation of a sulfide ligand
Lili Cao, Ulf Ryde
(2020) Journal of Catalysis, 391 p.247-259
Journal articleDoes the crystal structure of vanadium nitrogenase contain a reaction intermediate? Evidence from quantum refinement
Lili Cao, Octav Caldararu, Ulf Ryde
(2020) Journal of Biological Inorganic Chemistry, 25 p.847-861
Journal articleN2H2 binding to the nitrogenase FeMo cluster studied by QM/MM methods
Lili Cao, Ulf Ryde
(2020) Journal of Biological Inorganic Chemistry, 25 p.521-540
Journal articleFragHAR : Towards ab initio quantum-crystallographic X-ray structure refinement for polypeptides and proteins
Bergmann Justin, Max Davidson, Esko Oksanen, Ulf Ryde, Dylan Jayatilaka
(2020) IUCrJ, 7 p.158-165
Journal articleWater structure in solution and crystal molecular dynamics simulations compared to protein crystal structures
Octav Caldararu, Majda Misini Ignjatovic, Esko Oksanen, Ulf Ryde
(2020) RSC Advances, 10 p.8435-8443
Journal articleQuantum Mechanics/Molecular Mechanics Study of the Reaction Mechanism of Glyoxalase I
Sonia Jafari, Ulf Ryde, Adam Emad Ahmed Fouda, Fatemeh Sadat Alavi, Geng Dong, et al.
(2020) Inorganic Chemistry, 59 p.2594-2603
Journal articleBjärebjörnbär, ett nytt krypbjörnbär i Skåne
Mikael Hedrén, Mingyue Zhou, Melanie S. Montes, Ulf Ryde
(2020) Svensk Botanisk Tidskrift, 114 p.22-31
Journal articleWhat Is the Structure of the E4 Intermediate in Nitrogenase?
Lili Cao, Ulf Ryde
(2020) Journal of Chemical Theory and Computation, 16 p.1936-1952
Journal articleIs density functional theory accurate for lytic polysaccharide monooxygenase enzymes
Ernst D. Larsson, Geng Dong, Valera Veryazov, Ulf Ryde, Erik D. Hedegård
(2020) Dalton Transactions, 49 p.1501-1512
Journal articleImportance of the iron–sulfur component and of the siroheme modification in the resting state of sulfite reductase
Adrian M.V. Brânzanic, Ulf Ryde, Radu Silaghi-Dumitrescu
(2020) Journal of Inorganic Biochemistry, 203
Journal articleAutomated orientation of water molecules in neutron crystallographic structures of proteins
Axl Eriksson, Octav Caldararu, Ulf Ryde, Esko Oksanen
(2020) Acta Crystallographica Section D: Structural Biology, 76 p.1025-1032
Journal articleQuantum refinement with multiple conformations : Application to the P-cluster in nitrogenase
Lili Cao, Ulf Ryde
(2020) Acta Crystallographica Section D: Structural Biology, 76 p.1145-1156
Journal articleTheoretical insights into the aerobic hydrogenase activity of molybdenum-copper CO dehydrogenase
Anna Rovaletti, Maurizio Bruschi, Giorgio Moro, Ugo Cosentino, Claudio Greco, et al.
(2019) Inorganics, 7
Journal articleQM/MM study of the stereospecific proton exchange of glutathiohydroxyacetone by glyoxalase I
Sonia Jafari, Ulf Ryde, Mehdi Irani
(2019) Results in Chemistry, 1
Journal articleGeometry and Electronic Structure of the P-Cluster in Nitrogenase Studied by Combined Quantum Mechanical and Molecular Mechanical Calculations and Quantum Refinement
Lili Cao, Melanie C. Börner, Justin Bergmann, Octav Caldararu, Ulf Ryde
(2019) Inorganic Chemistry, 58 p.9672-9690
Journal articleStructure and Energetics of Ligand–Fluorine Interactions with Galectin-3 Backbone and Side-Chain Amides : Insight into Solvation Effects and Multipolar Interactions
Rohit Kumar, Majda Misini Ignjatović, Kristoffer Peterson, Martin Olsson, Hakon Leffler, et al.
(2019) ChemMedChem, 14 p.1528-1536
Journal articleSubstituted polyfluoroaryl interactions with an arginine side chain in galectin-3 are governed by steric-, desolvation and electronic conjugation effects
Rohit Kumar, Kristoffer Peterson, Majda Misini Ignjatović, Hakon Leffler, Ulf Ryde, et al.
(2019) Organic and Biomolecular Chemistry, 17 p.1081-1089
Journal articleRefinement of protein structures using a combination of quantum-mechanical calculations with neutron and X-ray crystallographic data
Octav Caldararu, Francesco Manzoni, Esko Oksanen, Derek T. Logan, Ulf Ryde
(2019) Acta Crystallographica Section D: Structural Biology, 75 p.368-380
Journal articleA thiocarbonate sink on the enzymatic energy landscape of aerobic CO oxidation? Answers from DFT and QM/MM models of Mo–Cu CO-dehydrogenases
Anna Rovaletti, Maurizio Bruschi, Giorgio Moro, Ugo Cosentino, Ulf Ryde, et al.
(2019) Journal of Catalysis , p.201-205
Journal articleHost-Guest Relative Binding Affinities at Density-Functional Theory Level from Semiempirical Molecular Dynamics Simulations
Meiting Wang, Ye Mei, Ulf Ryde
(2019) Journal of Chemical Theory and Computation, 15 p.2659-2671
Journal articleExtremely large differences in DFT energies for nitrogenase models
Lili Cao, Ulf Ryde
(2019) Physical Chemistry Chemical Physics, 21 p.2480-2488
Journal articleMechanism of hydrogen peroxide formation by lytic polysaccharide monooxygenase
Octav Caldararu, Esko Oksanen, Ulf Ryde, Erik D. Hedegård
(2019) Chemical Science, 10 p.576-586
Journal articleQM/MM study of the conversion of biliverdin into verdoheme by heme oxygenase
Fatemeh Sadat Alavi, Mansour Zahedi, Nasser Safari, Ulf Ryde
(2019) Theoretical Chemistry Accounts, 138
Journal articleInterplay between Conformational Entropy and Solvation Entropy in Protein-Ligand Binding
Maria Luisa Verteramo, Olof Stenström, Majda Misini Ignjatović, Octav Caldararu, Martin A. Olsson, et al.
(2019) Journal of the American Chemical Society, 141 p.2012-2026
Journal articleAre crystallographic : B-factors suitable for calculating protein conformational entropy?
Octav Caldararu, Rohit Kumar, Esko Oksanen, Derek T. Logan, Ulf Ryde
(2019) Physical Chemistry Chemical Physics, 21 p.18149-18160
Journal articleWhy does sulfite reductase employ siroheme?
Adrian M.V. Brânzanic, Ulf Ryde, Radu Silaghi-Dumitrescu
(2019) Chemical Communications, 55 p.14047-14049
Journal articleQM/MM study of the reaction mechanism of sulfite oxidase
Octav Caldararu, Milica Feldt, Daniela Cioloboc, Marie Céline Van Severen, Kerstin Starke, et al.
(2018) Scientific Reports, 8
Journal articleReaction mechanism of formate dehydrogenase studied by computational methods
Geng Dong, Ulf Ryde
(2018) Journal of Biological Inorganic Chemistry, 23 p.1243-1254
Journal articlePredicting Relative Binding Affinity Using Nonequilibrium QM/MM Simulations
Meiting Wang, Ye Mei, Ulf Ryde
(2018) Journal of Chemical Theory and Computation, 14 p.6613-6613
Journal articleBinding free energies in the SAMPL6 octa-acid host–guest challenge calculated with MM and QM methods
Octav Caldararu, Martin A. Olsson, Majda Misini Ignjatović, Meiting Wang, Ulf Ryde
(2018) Journal of Computer-Aided Molecular Design, 32 p.1027-1046
Journal articleRelative Ligand-Binding Free Energies Calculated from Multiple Short QM/MM MD Simulations
Ulf Ryde, Martin Olsson, Casper Steinmann
(2018) Journal of Chemical Theory and Computation, 14 p.3228-3228
Journal articleHigher Flexibility of Glu-172 Explains the Unusual Stereospecificity of Glyoxalase i
Sonia Jafari, Nadia Kazemi, Ulf Ryde, Mehdi Irani
(2018) Inorganic Chemistry, 57 p.4944-4958
Journal articleOn the difference between additive and subtractive QM/MM calculations
Lili Cao, Ulf Ryde
(2018) Frontiers in Chemistry, 6
Journal articleMolecular mechanism of lytic polysaccharide monooxygenases
Erik Hedegård, Ulf Ryde
(2018) Chemical Science, 9 p.3866-3880
Journal articleCan MM/GBSA calculations be sped up by system truncation?
Majda Misini Ignjatović, Paulius Mikulskis, Pär Söderhjelm, Ulf Ryde
(2018) Journal of Computational Chemistry, 39 p.361-372
Journal articleInfluence of the protein and DFT method on the broken-symmetry and spin states in nitroge
Lili Cao, Ulf Ryde
(2018) International Journal of Quantum Chemistry, 118 p.1-1
Journal articleAssessing the stability of free-energy perturbation calculations by performing variations in the method
Francesco Manzoni, Ulf Ryde
(2018) Journal of Computer-Aided Molecular Design, 32 p.529-536
Journal articleInsight into the reaction mechanism of lipoyl synthase : a QM/MM study
Geng Dong, Lili Cao, Ulf Ryde
(2018) Journal of Biological Inorganic Chemistry, 23 p.221-229
Journal articleQuantum Crystallography: Current Developments and Future Perspectives
Alessandro Genoni, Lukas Bučinský, Nicolas Claiser, Julia Contreras‐García, Birger Dittrich, et al.
(2018) Chemistry: A European Journal, 24 p.10881-10905
Journal articleQuantum Refinement Does Not Support Dinuclear Copper Sites in Crystal Structures of Particulate Methane Monooxygenase
Lili Cao, Octav Caldararu, Amy C. Rosenzweig, Ulf Ryde
(2018) Angewandte Chemie - International Edition, 57 p.162-166
Journal articleA novel mechanism of heme degradation to biliverdin studied by QM/MM and QM calculations
Fatemeh Sadat Alavi, Mahin Gheidi, Mansour Zahedi, Nasser Safari, Ulf Ryde
(2018) Dalton Transactions, 47 p.8283-8291
Journal articleBinding affinities of the farnesoid X receptor in the D3R Grand Challenge 2 estimated by free-energy perturbation and docking
Martin A. Olsson, Alfonso T. García-Sosa, Ulf Ryde
(2018) Journal of Computer-Aided Molecular Design, 32 p.211-224
Journal articleExploration of H2 binding to the [NiFe]-hydrogenase active site with multiconfigurational density functional theory
Geng Dong, Ulf Ryde, Hans Jørgen Aa Jensen, Erik D. Hedegård
(2018) Physical Chemistry Chemical Physics, 20 p.794-801
Journal articleReaction Mechanism of [NiFe] Hydrogenase Studied by Computational Methods
Geng Dong, Quan Manh Phung, Kristine Pierloot, Ulf Ryde
(2018) Inorganic Chemistry, 57 p.15289-15298
Journal articleProtonation and Reduction of the FeMo Cluster in Nitrogenase Studied by Quantum Mechanics/Molecular Mechanics (QM/MM) Calculations
Lili Cao, Octav Caldararu, Ulf Ryde
(2018) Journal of Chemical Theory and Computation, 14 p.6653-6678
Journal articleQM/MM Study of the Conversion of Oxophlorin into Verdoheme by Heme Oxygenase
Fatemeh Sadat Alavi, Mansour Zahedi, Nasser Safari, Ulf Ryde
(2017) Journal of Physical Chemistry B, 121 p.11427-11436
Journal articleCan System Truncation Speed up Ligand-Binding Calculations with Periodic Free-Energy Simulations?
Francesco Manzoni, Jon Uranga, Samuel Genheden, Ulf Ryde
(2017) Journal of Chemical Information and Modeling, 57 p.2865-2873
Journal articleHow Many Conformations Need to Be Sampled to Obtain Converged QM/MM Energies? the Curse of Exponential Averaging
Ulf Ryde
(2017) Journal of Chemical Theory and Computation, 13 p.5745-5752
Journal articleProtonation States of Homocitrate and Nearby Residues in Nitrogenase Studied by Computational Methods and Quantum Refinement
Lili Cao, Octav Caldararu, Ulf Ryde
(2017) Journal of Physical Chemistry B, 121 p.8242-8262
Journal articleEffect of the protein ligand in DMSO reductase studied by computational methods
Geng Dong, Ulf Ryde
(2017) Journal of Inorganic Biochemistry, 171 p.45-51
Journal articleComparison of QM/MM Methods To Obtain Ligand-Binding Free Energies
Martin A. Olsson, Ulf Ryde
(2017) Journal of Chemical Theory and Computation, 13 p.2245-2253
Journal articleBinding free energies in the SAMPL5 octa-acid host–guest challenge calculated with DFT-D3 and CCSD(T)
Octav Caldararu, Martin A. Olsson, Christoph Riplinger, Frank Neese, Ulf Ryde
(2017) Journal of Computer-Aided Molecular Design, 31 p.87-106
Journal articleMultiscale Modelling of Lytic Polysaccharide Monooxygenases
Erik Hedegård, Ulf Ryde
(2017) ACS Omega, 2 p.536-545
Journal articleTargeting the reactive intermediate in polysaccharide monooxygenases
Erik Hedegård, Ulf Ryde
(2017) Journal of Biological Inorganic Chemistry
Journal articleH2 binding to the active site of [NiFe] hydrogenase studied by multiconfigurational and coupled-cluster methods
Geng Dong, Quan Manh Phung, Simon D. Hallaert, Kristine Pierloot, Ulf Ryde
(2017) Physical Chemistry Chemical Physics, 19 p.10590-10601
Journal articleO2 activation in salicylate 1,2-dioxygenase : A QM/MM study reveals the role of His162
Geng Dong, Ulf Ryde
(2016) Inorganic Chemistry, 55 p.11727-11735
Journal articleDoes the DFT Self-Interaction Error Affect Energies Calculated in Proteins with Large QM Systems?
Adam Fouda, Ulf Ryde
(2016) Journal of Chemical Theory and Computation, 12 p.5667-5679
Journal articleComputational Studies of Molybdenum and Tungsten Enzymes
Ulf Ryde, Geng Dong, Jilai Li, Milica Feldt, Ricardo A Mata
(2016) RSC Metallobiology, 2017-January p.275-321
Book chapterCatalytic mechanism of human glyoxalase i studied by quantum-mechanical cluster calculations
Sonia Jafari, Ulf Ryde, Mehdi Irani
(2016) Journal of Molecular Catalysis B: Enzymatic, 131 p.18-30
Journal articleBinding-affinity predictions of HSP90 in the D3R Grand Challenge 2015 with docking, MM/GBSA, QM/MM, and free-energy simulations
Majda Misini Ignjatović, Octav Caldararu, Geng Dong, Camila Muñoz-Gutierrez, Francisco Adasme-Carreño, et al.
(2016) Journal of Computer-Aided Molecular Design, 30 p.707-730
Journal articleConverging ligand-binding free energies obtained with free-energy perturbations at the quantum mechanical level
Martin A. Olsson, Pär Söderhjelm, Ulf Ryde
(2016) Journal of Computational Chemistry, 37 p.1589-1600
Journal articleLigand-Binding Affinity Estimates Supported by Quantum-Mechanical Methods
Ulf Ryde, Pär Söderhjelm
(2016) Chemical Reviews, 116 p.5520-5566
Journal articleProtonation states of intermediates in the reaction mechanism of [NiFe] hydrogenase studied by computational methods.
Geng Dong, Ulf Ryde
(2016) Journal of Biological Inorganic Chemistry, 21 p.383-394
Journal articleBinding affinities by alchemical perturbation using QM/MM with a large QM system and polarizable MM model.
Samuel Genheden, Ulf Ryde, Pär Söderhjelm
(2015) Journal of Computational Chemistry, 36 p.2114-2124
Journal articleCatalytic Cycle of Multicopper Oxidases Studied by Combined Quantum- and Molecular-Mechanical Free-Energy Perturbation Methods.
Jilai Li, Maryam Farrokhnia, Lubomir Rulisek, Ulf Ryde
(2015) The Journal of Physical Chemistry Part B, 119 p.8268-8284
Journal articleSimulation of the isotropic EXAFS spectra for the S2 and S3 structures of the oxygen evolving complex in photosystem II.
Xichen Li, Per E M Siegbahn, Ulf Ryde
(2015) Proceedings of the National Academy of Sciences, 112 p.3979-3984
Journal articleThe MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities
Samuel Genheden, Ulf Ryde
(2015) Expert Opinion on Drug Discovery, 10 p.449-461
Journal article reviewA Computational Comparison of Oxygen Atom Transfer Catalyzed by Dimethyl Sulfoxide Reductase with Mo and W
Jilai Li, Milica Andrejic, Ricardo A. Mata, Ulf Ryde
(2015) European Journal of Inorganic Chemistry , p.3580-3589
Journal articleMultiscale Modeling of the Active Site of [Fe] Hydrogenase: The H-2 Binding Site in Open and Closed Protein Conformations
Erik Donovan Hedegard, Jacob Kongsted, Ulf Ryde
(2015) Angewandte Chemie (International edition), 54 p.6246-6250
Journal articleAccurate calculations of geometries and singlet-triplet energy differences for active-site models of [NiFe] hydrogenase
Mickael G. Delcey, Kristine Pierloot, Quan M. Phung, Steven Vancoillie, Roland Lindh, et al.
(2014) Physical Chemistry Chemical Physics, 16 p.7927-7938
Journal articleComparison of the active-site design of molybdenum oxo-transfer enzymes by quantum mechanical calculations.
Jilai Li, Ulf Ryde
(2014) Inorganic Chemistry, 53 p.11913-11924
Journal articleCoupled-Cluster Interaction Energies for 200-Atom Host-Guest Systems
Milica Andrejic, Ulf Ryde, Ricardo A. Mata, Pär Söderhjelm
(2014) ChemPhysChem, 15 p.3270-3281
Journal articleTheoretical Fe-57 Mossbauer spectroscopy: isomer shifts of [Fe]- hydrogenase intermediates
Erik Donovan Hedegard, Stefan Knecht, Ulf Ryde, Jacob Kongsted, Trond Saue
(2014) Physical Chemistry Chemical Physics, 16 p.4853-4863
Journal articleFree-energy perturbation and quantum mechanical study of SAMPL4 octa-acid host-guest binding energies.
Paulius Mikulskis, Daniela Cioloboc, Milica Andrejić, Sakshi Khare, Joakim Brorsson, et al.
(2014) Journal of Computer-Aided Molecular Design, 28 p.375-400
Journal articleThe neutron structure of urate oxidase resolves a long-standing mechanistic conundrum and reveals unexpected changes in protonation.
Esko Oksanen, Matthew P Blakeley, Mohamed El-Hajji, Ulf Ryde, Monika Budayova-Spano
(2014) PLoS ONE, 9
Journal articleA quantum-mechanical study of the reaction mechanism of sulfite oxidase.
Marie-Céline Van Severen, Milica Andrejić, Jilai Li, Kerstin Starke, Ricardo A Mata, et al.
(2014) Journal of Biological Inorganic Chemistry, 19 p.1165-1179
Journal articleLarge Equatorial Ligand Effects on C-H Bond Activation by Nonheme Iron(IV)-oxo Complexes
Xiaoli Sun, Caiyun Geng, Ruiping Huo, Ulf Ryde, Yuxiang Bu, et al.
(2014) The Journal of Physical Chemistry Part B, 118 p.1493-1500
Journal articleA fundamental view of enthalpy-entropy compensation
Ulf Ryde
(2014) MedChemComm, 5 p.1324-1336
Journal articleA Large-Scale Test of Free-Energy Simulation Estimates of Protein-Ligand Binding Affinities.
Paulius Mikulskis, Samuel Genheden, Ulf Ryde
(2014) Journal of Chemical Information and Modeling, 54 p.2794-2806
Journal articleEffect of explicit water molecules on ligand-binding affinities calculated with the MM/GBSA approach.
Paulius Mikulskis, Samuel Genheden, Ulf Ryde
(2014) Journal of Molecular Modeling, 20 p.2273-2273
Journal articleConformational Entropies and Order Parameters: Convergence, Reproducibility, and Transferability
Samuel Genheden, Mikael Akke, Ulf Ryde
(2014) Journal of Chemical Theory and Computation, 10 p.432-438
Journal articleComputational modelling of oxygenation processes in enzymes and biomimetic model complexes
Sam P. de Visser, Matthew G. Quesne, Bodo Martin, Peter Comba, Ulf Ryde
(2014) Chemical Communications, 50 p.262-282
Journal article reviewTheoretical EXAFS studies of a model of the oxygen-evolving complex of photosystem II obtained with the quantum cluster approach
Xichen Li, Eduardo M. Sproviero, Ulf Ryde, Victor S. Batista, Guangju Chen
(2013) International Journal of Quantum Chemistry, 113 p.474-478
Journal articleTheoretical Studies of the Active-Site Structure, Spectroscopic and Thermodynamic Properties, and Reaction Mechanism of Multicopper Oxidases
Lubomir Rulisek, Ulf Ryde
(2013) Coordination Chemistry Reviews, 257 p.445-458
Journal article reviewUnderstanding the Chemistry of Lead at a Molecular Level: The Pb(II) 6s6p Lone Pair Can Be Bisdirected in Proteins
Marie-Celine Van Severen, Ulf Ryde, Olivier Parisel, Jean-Philip Piquernal
(2013) Journal of Chemical Theory and Computation, 9 p.2416-2424
Journal articleHow are hydrogen bonds modified by metal binding?
Charlotte Husberg, Ulf Ryde
(2013) Journal of Biological Inorganic Chemistry, 18 p.499-522
Journal articleAccurate reaction energies in proteins obtained by combining QM/MM and large QM calculations
LiHong Hu, Pär Söderhjelm, Ulf Ryde
(2013) Journal of Chemical Theory and Computation, 9 p.640-649
Journal articleEffect of geometry optimisations on QM-cluster and QM/MM studies of reaction energies in proteins
Sophie Sumner, Pär Söderhjelm, Ulf Ryde
(2013) Journal of Chemical Theory and Computation, 9 p.4205-4214
Journal articleLarge Density-Functional and Basis-Set Effects for the DMSO Reductase Catalyzed Oxo-Transfer Reaction
Jilai Li, Ricardo A. Mata, Ulf Ryde
(2013) Journal of Chemical Theory and Computation, 9 p.1799-1807
Journal articleAmino Acid Oxidation of Candida antarctica Lipase B Studied by Molecular Dynamics Simulations and Site-Directed Mutagenesis
Mehdi Irani, Ulrika Törnvall, Samuel Genheden, Marianne Wittrup Larsen, Rajni Hatti-Kaul, et al.
(2013) Biochemistry, 52 p.1280-1289
Journal articleComparison of MM/GBSA calculations based on explicit and implicit solvent simulations.
Frithjof Godschalk, Samuel Genheden, Pär Söderhjelm, Ulf Ryde
(2013) Physical Chemistry Chemical Physics, 15 p.7731-7739
Journal articleQuantum mechanics in structure-based ligand design
Pär Söderhjelm, Samuel Genheden, Ulf Ryde
(2012) Methods and principles in medicinal chemistry, 53 p.121-143
Book chapterThe Normal-Mode Entropy in the MM/GBSA Method: Effect of System Truncation, Buffer Region, and Dielectric Constant
Samuel Genheden, Oliver Kuhn, Paulius Mikulskis, Daniel Hoffmann, Ulf Ryde
(2012) Journal of Chemical Information and Modeling, 52 p.2079-2088
Journal articleQuantum-mechanical studies of reactions performed by cytochrome P450 enzymes
Patrik Rydberg, Lars Olsen, Ulf Ryde
(2012) Current Inorganic Chemistry, 2 p.292-315
Journal article reviewTransferability of conformational dependent charges from protein simulations
Samuel Genheden, Pär Söderhjelm, Ulf Ryde
(2012) International Journal of Quantum Chemistry, 112 p.1768-1785
Journal articleWill molecular dynamics simulations of proteins ever reach equilibrium?
Samuel Genheden, Ulf Ryde
(2012) Physical chemistry chemical physics : PCCP, 14 p.8662-8677
Journal articleOn the Possibility of Uphill Intramolecular Electron Transfer in Multicopper Oxidases: Electrochemical and Quantum Chemical Study of Bilirubin Oxidase
Sergey Shleev, Viktor Andoralov, Magnus Falk, Curt Reimann, Tautgirdas Ruzgas, et al.
(2012) Electroanalysis, 24 p.1524-1540
Journal articleComparison of end-point continuum-solvation methods for the calculation of protein-ligand binding free energies.
Samuel Genheden, Ulf Ryde
(2012) Proteins, 80 p.1326-1342
Journal articleConvergence of QM/MM free-energy perturbations based on molecular-mechanics or semiempirical simulations.
Jimmy Heimdal, Ulf Ryde
(2012) Physical chemistry chemical physics : PCCP, 14 p.12592-12604
Journal articleImproving the Efficiency of Protein-Ligand Binding Free-Energy Calculations by System Truncation
Samuel Genheden, Ulf Ryde
(2012) Journal of Chemical Theory and Computation, 8 p.1449-1458
Journal articleThe Carbohydrate-Binding Site in Galectin-3 Is Preorganized To Recognize a Sugarlike Framework of Oxygens: Ultra-High-Resolution Structures and Water Dynamics
Saraboji Kadhirvel, Maria Håkansson, Samuel Genheden, Carl Diehl, Johan Qvist, et al.
(2012) Biochemistry, 51 p.296-306
Journal articleA semiempirical approach to ligand-binding affinities: Dependence on the Hamiltonian and corrections.
Paulius Mikulskis, Samuel Genheden, Karin Wichmann, Ulf Ryde
(2012) Journal of Computational Chemistry, 33 p.1179-1189
Journal articleBinding affinities in the SAMPL3 trypsin and host-guest blind tests estimated with the MM/PBSA and LIE methods.
Paulius Mikulskis, Samuel Genheden, Patrik Rydberg, Lars Sandberg, Lars Olsen, et al.
(2012) Journal of Computer-Aided Molecular Design, 26 p.527-541
Journal articleCan the protonation state of histidine residues be determined from molecular dynamics simulations?
Jon Uranga, Paulius Mikulskis, Samuel Genheden, Ulf Ryde
(2012) Computational and Theoretical Chemistry, 1000 p.75-84
Journal articleTargeting Intermediates of [FeFe]-Hydrogenase by CO and CN Vibrational Signatures
Lian Yu, Claudio Greco, Maurizio Bruschi, Ulf Ryde, Luca De Gioia, et al.
(2011) Inorganic Chemistry, 50 p.3888-3900
Journal articleReduction Potentials and Acidity Constants of Mn Superoxide Dismutase Calculated by QM/MM Free-Energy Methods.
Jimmy Heimdal, Markus Kaukonen, Martin Srnec, Lubomir Rulisek, Ulf Ryde
(2011) ChemPhysChem, 12 p.3337-3347
Journal articleUnraveling the similarity of the photoabsorption of deprotonated p-coumaric acid in the gas phase and within the photoactive yellow protein
Tomas Rocha-Rinza, Kristian Sneskov, Ove Christiansen, Ulf Ryde, Jacob Kongsted
(2011) Physical Chemistry Chemical Physics, 13 p.1585-1589
Journal articleMechanistic and Physiological Implications of the Interplay among Iron-Sulfur Clusters in [FeFe]-Hydrogenases. A QM/MM Perspective
Claudio Greco, Maurizio Bruschi, Piercarlo Fantucci, Ulf Ryde, Luca De Gioia
(2011) Journal of the American Chemical Society, 133 p.18742-18749
Journal articleA comparison of different initialization protocols to obtain statistically independent molecular dynamics simulations.
Samuel Genheden, Ulf Ryde
(2011) Journal of Computational Chemistry, 32 p.187-195
Journal articleReorganization Energy for Internal Electron Transfer in Multicopper Oxidases.
LiHong Hu, Maryam Farrokhnia, Jimmy Heimdal, Sergey Shleev, Lubomir Rulisek, et al.
(2011) The Journal of Physical Chemistry Part B, 115 p.13111-13126
Journal articleA QM/MM study of the binding of RAPTA ligands to cathepsin B
Antonella Ciancetta, Samuel Genheden, Ulf Ryde
(2011) Journal of Computer-Aided Molecular Design, 25 p.729-742
Journal articleIsocyanide in Biochemistry? A Theoretical Investigation of the Electronic Effects and Energetics of Cyanide Ligand Protonation in [FeFe]-Hydrogenases
Claudio Greco, Maurizio Bruschi, Piercarlo Fantucci, Ulf Ryde, Luca De Gioia
(2011) Chemistry: A European Journal, 17 p.1954-1965
Journal articleReductive cleavage of the O-O bond in multicopper oxidases: a QM/MM and QM study
Martin Srnec, Ulf Ryde, Lubomir Rulisek
(2011) Faraday Discussions, 148 p.41-53
Journal articleAccurate Predictions of Nonpolar Solvation Free Energies Require Explicit Consideration of Binding-Site Hydration
Samuel Genheden, Paulius Mikulskis, LiHong Hu, Jacob Kongsted, Pär Söderhjelm, et al.
(2011) Journal of the American Chemical Society, 133 p.13081-13092
Journal articleProbing 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.
Claudio Greco, Maurizio Bruschi, Piercarlo Fantucci, Ulf Ryde, Luca De Gioia
(2011) ChemPhysChem, 12 p.3376-3382
Journal articleFast Generation of Broken-Symmetry States in a Large System Including Multiple Iron-Sulfur Assemblies: Investigation of QM/MM Energies, Clusters Charges, and Spin Populations
Claudio Greco, Piercarlo Fantucci, Ulf Ryde, Luca de Gioia
(2011) International Journal of Quantum Chemistry, 111 p.3949-3960
Journal articleArguments for a narrow species concept in Rubus sect. Corylifolii
Ulf Ryde
(2011) Nordic Journal of Botany, 29 p.708-721
Journal articleComparison of the Efficiency of the LIE and MM/GBSA Methods to Calculate Ligand-Binding Energies
Samuel Genheden, Ulf Ryde
(2011) Journal of Chemical Theory and Computation, 7 p.3768-3778
Journal articleDoes DFT-D estimate accurate energies for the binding of ligands to metal complexes?
Ulf Ryde, Ricardo A Mata, Stefan Grimme
(2011) Dalton Transactions, 40 p.11176-11183
Journal articleConformational Dependence of Isotropic Polarizabilities
Pär Söderhjelm, Jacob Kongsted, Ulf Ryde
(2011) Journal of Chemical Theory and Computation, 7 p.1404-1414
Journal articleOn the Convergence of QM/MM Energies
LiHong Hu, Paer Soederhjelm, Ulf Ryde
(2011) Journal of Chemical Theory and Computation, 7 p.761-777
Journal articleBinding Affinities of Factor Xa Inhibitors Estimated by Thermodynamic Integration and MM/GBSA.
Samuel Genheden, Ingemar Nilsson, Ulf Ryde
(2011) Journal of Chemical Information and Modeling, 51 p.947-958
Journal articleComparison of Methods to Obtain Force-Field Parameters for Metal Sites
LiHong Hu, Ulf Ryde
(2011) Journal of Chemical Theory and Computation, 7 p.2452-2463
Journal articleMagnetic Properties of [FeFe]-Hydrogenases: A Theoretical Investigation Based on Extended QM and QM/MM Models of the H-Cluster and Its Surroundings
Claudio Greco, Alexey Silakov, Maurizio Bruschi, Ulf Ryde, Luca De Gioia, et al.
(2011) European Journal of Inorganic Chemistry , p.1043-1049
Journal articleGenetic analysis shows that Rubus vikensis is a distinct species with a disjunct distribution
Ulf Ryde
(2010) Nordic Journal of Botany, 28 p.246-250
Journal articleHow to obtain statistically converged MM/GBSA results.
Samuel Genheden, Ulf Ryde
(2010) Journal of Computational Chemistry, 31 p.837-846
Journal articleA five-coordinate [2Fe-2S] cluster.
Michael G G Fuchs, Sebastian Dechert, Serhiy Demeshko, Ulf Ryde, Franc Meyer
(2010) Inorganic Chemistry, 49 p.5853-5858
Journal articleProtein Flexibility and Conformational Entropy in Ligand Design Targeting the Carbohydrate Recognition Domain of Galectin-3.
Carl Diehl, Olof Engström, Tamara Delaine, Maria Håkansson, Samuel Genheden, et al.
(2010) Journal of the American Chemical Society, 132 p.14577-14589
Journal articleAn MM/3D-RISM approach for ligand binding affinities.
Samuel Genheden, Tyler Luchko, Sergey Gusarov, Andriy Kovalenko, Ulf Ryde
(2010) The Journal of Physical Chemistry Part B, 114 p.8505-8516
Journal articleEstimates of ligand-binding affinities supported by quantum mechanical methods.
Pär Söderhjelm, Jacob Kongsted, Samuel Genheden, Ulf Ryde
(2010) Interdisciplinary sciences, computational life sciences, 2 p.21-37
Journal articleFunctionally Relevant Interplay between the Fe(4)S(4) Cluster and CN(-) Ligands in the Active Site of [FeFe]-Hydrogenases.
Maurizio Bruschi, Claudio Greco, Luca Bertini, Piercarlo Fantucci, Ulf Ryde, et al.
(2010) Journal of the American Chemical Society, 132 p.4992-4992
Journal articleQuantum refinement of [FeFe] hydrogenase indicates a dithiomethylamine ligand
Ulf Ryde, Claudio Greco, Luca De Gioia
(2010) Journal of the American Chemical Society, 132 p.4512-4512
Journal articleMultireference Ab Initio Calculations of g tensors for Trinuclear Copper Clusters in Multicopper Oxidases.
Steven Vancoillie, Jakub Chalupský, Ulf Ryde, Edward I Solomon, Kristine Pierloot, et al.
(2010) The Journal of Physical Chemistry Part B, 114 p.7692-7702
Journal articleA combined computational and experimental investigation of the [2Fe-2S] cluster in biotin synthase
Michael G. G. Fuchs, Franc Meyer, Ulf Ryde
(2010) Journal of Biological Inorganic Chemistry, 15 p.203-212
Journal articleStarting-Condition Dependence of Order Parameters Derived from Molecular Dynamics Simulations
Samuel Genheden, Carl Diehl, Mikael Akke, Ulf Ryde
(2010) Journal of Chemical Theory and Computation, 6 p.2176-2190
Journal articleNonpolar Solvation Free Energies of Protein-Ligand Complexes
Samuel Genheden, Jacob Kongsted, Pär Söderhjelm, Ulf Ryde
(2010) Journal of Chemical Theory and Computation, 6 p.3558-3568
Journal articleLigand affinities estimated by quantum chemical calculations
Pär Söderhjelm, Jacob Kongsted, Ulf Ryde
(2010) Journal of Chemical Theory and Computation, 6 p.1726-1737
Journal articleRubus sordirosanthus in Halland, southwest Sweden
Ulf Ryde, Gun Werlemark
(2010) Svensk Botanisk Tidskrift, 104 p.405-413
Journal articleConformational dependence of charges in protein simulations
Pär Söderhjelm, Ulf Ryde
(2009) Journal of Computational Chemistry, 30 p.750-760
Journal articleInfluence 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
Maurizio Bruschi, Claudio Greco, Markus Kaukonen, Piercarlo Fantucci, Ulf Ryde, et al.
(2009) Angewandte Chemie (International edition), 48 p.3503-3506
Journal articleHow Accurate Can a Force Field Become? A Polarizable Multipole Model Combined with Fragment-wise Quantum-Mechanical Calculations
Pär Söderhjelm, Ulf Ryde
(2009) Journal of physical chemistry. A, 113 p.617-627
Journal articleAn improved method to predict the entropy term with the MM/PBSA approach.
Jacob Kongsted, Ulf Ryde
(2009) Journal of Computer-Aided Molecular Design, 23 p.63-71
Journal articleProtein Influence on Electronic Spectra Modeled by Multipoles and Polarizabilities
Pär Söderhjelm, Charlotte Husberg, Angela Strambi, Massimo Olivucci, Ulf Ryde
(2009) Journal of Chemical Theory and Computation, 5 p.649-658
Journal articleConformational entropy changes upon lactose binding to the carbohydrate recognition domain of galectin-3.
Carl Diehl, Samuel Genheden, Kristofer Modig, Ulf Ryde, Mikael Akke
(2009) Journal of Biomolecular NMR, 45 p.157-169
Journal articleHow accurate are continuum solvation models for drug-like molecules?
Jacob Kongsted, Pär Söderhjelm, Ulf Ryde
(2009) Journal of Computer-Aided Molecular Design, 23 p.395-409
Journal articleRubus sect. Corylifolii in the province of Halland, SW Sweden
Ulf Ryde
(2009) Svensk Botanisk Tidskrift, 103 p.279-300
Journal articleCalculation of Protein-Ligand Interaction Energies by a Fragmentation Approach Combining High-Level Quantum Chemistry with Classical Many-Body Effects
Pär Söderhjelm, Francesco Aquilante, Ulf Ryde
(2009) The Journal of Physical Chemistry Part B, 113 p.11085-11094
Journal articleQM/MM study of the insertion of metal ion into protoporphyrin IX by ferrochelatase
Yaxue Wang, Yong Shen, Ulf Ryde
(2009) Journal of Inorganic Biochemistry, 103 p.1680-1686
Journal articleReaction Mechanism of Manganese Superoxide Dismutase Studied by Combined Quantum and Molecular Mechanical Calculations and Multiconfigurational Methods.
Martin Srnec, Francesco Aquilante, Ulf Ryde, Lubomír Rulíšek
(2009) The Journal of Physical Chemistry Part B, 113 p.6074-6086
Journal articleCobalamins uncovered by modern electronic structure calculations
Kasper Jensen, Ulf Ryde
(2009) Coordination Chemistry Reviews, 253 p.769-778
Journal article reviewStudies 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
Giorgio Zoppellaro, Kara L. Bren, Amy A. Ensign, Espen Harbitz, Ravinder Kaur, et al.
(2009) Biopolymers, 91 p.1064-1082
Journal article reviewDo quantum mechanical energies calculated for small models of protein-active sites converge?
LiHong Hu, Jenny Eliasson, Jimmy Heimdal, Ulf Ryde
(2009) Journal of physical chemistry. A, 113 p.11793-11800
Journal articleQuantum mechanical/molecular mechanical (QM/MM) methods and applications in bioinorganic chemistry
Ulf Ryde
(2009) Computational inorganic and bioinorganic chemistry , p.33-42
Book chapterWhich 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.
Ulf Ryde, Carola Schulzke, Kerstin Starke
(2009) Journal of Biological Inorganic Chemistry, 14 p.1053-1064
Journal articleA DFT investigation on structural and redox properties of a synthetic Fe6S6 assembly closely related to the [FeFe]-hydrogenases active site
Maurizio Bruschi, Claudio Greco, Giuseppe Zampella, Ulf Ryde, Christopher J. Pickett, et al.
(2008) Comptes Rendus. Chimie, 11 p.834-841
Journal articleProtonation of the proximal histidine ligand in heme peroxidases.
Jimmy Heimdal, Patrik Rydberg, Ulf Ryde
(2008) The Journal of Physical Chemistry Part B, 112 p.2501-2510
Journal articleSecondary bonding interactions in biomimetic [2Fe-2S] clusters
Joachim Ballmann, Sebastian Dechert, Eckhard Bill, Ulf Ryde, Franc Meyer
(2008) Inorganic Chemistry, 47 p.1586-1596
Journal articlePrediction of Activation Energies for Aromatic Oxidation by Cytochrome P450
Patrik Rydberg, Ulf Ryde, Lars Olsen
(2008) The Journal of Physical Chemistry Part A: Molecules, Spectroscopy, Kinetics, Environment and General Theory, 112 p.13058-13065
Journal articleA comparison of the tetrapyrrole cofactors in nature and their tuning by axial ligands
Kasper P. Jensen, Patrik Rydberg, Jimmy Heimdal, Ulf Ryde
(2008) Computational modeling for homogeneous and enzymatic catalysis , p.27-56
Book chapterThe Influence of X-Rays on the Structural Studies of Peroxide-Derived Myoglobin Intermediates
Hans-Petter Hersleth, Ya-Wen Hsiao, Ulf Ryde, Carl Henrik Gorbitz, K. Kristoffer Andersson
(2008) Chemistry and Biodiversity, 5 p.2067-2089
Journal article reviewTransition-state docking of flunitrazepam and progesterone in cytochrome P450
Patrik Rydberg, Sine Myrup Hansen, Jacob Kongsted, Per-Ola Norrby, Lars Olsen, et al.
(2008) Journal of Chemical Theory and Computation, 4 p.673-681
Journal articleSulfoxide, sulfur, and nitrogen oxidation and dealkylation by cytochrome P450
Patrik Rydberg, Ulf Ryde, Lars Olsen
(2008) Journal of Chemical Theory and Computation, 4 p.1369-1377
Journal articleThe crystal structure of peroxymyoglobin generated through cryoradiolytic reduction of myoglobin compound III during data collection
Hans-Petter Hersleth, Ya-Wen Hsiao, Ulf Ryde, Carl Henrik Gorbitz, K. Kristoffer Andersson
(2008) Biochemical Journal, 412 p.257-264
Journal articleAccuracy of typical approximations in classical models of intermolecular polarization
Pär Söderhjelm, Anders Öhrn, Ulf Ryde, Gunnar Karlström
(2008) Journal of Chemical Physics, 128
Journal articleQM/MM-PBSA method to estimate free energies for reactions in proteins
Markus Kaukonen, Pär Söderhjelm, Jimmy Heimdal, Ulf Ryde
(2008) The Journal of Physical Chemistry Part B, 112 p.12537-12548
Journal articleProton transfer at metal sites in proteins studied by quantum mechanical free-energy perturbations
Markus Kaukonen, Pär Söderhjelm, Jimmy Heimdal, Ulf Ryde
(2008) Journal of Chemical Theory and Computation, 4 p.985-1001
Journal articleEffect of covalent links on the structure, spectra, and redox properties of myeloperoxidase - A density functional study.
Ajitha Devarajan, Alexander Gaenko, Ulf Ryde
(2008) Journal of Inorganic Biochemistry, 102 p.1549-1557
Journal articleA Synthetic Analogue of Rieske-Type [2Fe-2S] Clusters
Joachim Ballmann, Antonia Albers, Serhiy Demeshko, Sebastian Dechert, Eckhard Bill, et al.
(2008) Angewandte Chemie (International edition), 47 p.9537-9541
Journal articleGeneral transition-state force field for cytochrome p450 Hydroxylation
Patrik Rydberg, Lars Olsen, Per-Ola Norrby, Ulf Ryde
(2007) Journal of Chemical Theory and Computation, 3 p.1765-1773
Journal articleAccuracy of distributed multipoles and polarizabilities: Comparison between the LoProp and MpProp models
Pär Söderhjelm, Jesper Wisborg Krogh, Gunnar Karlström, Ulf Ryde, Roland Lindh
(2007) Journal of Computational Chemistry, 28 p.1083-1090
Journal articleDynamics of water molecules in the active-site cavity of human cytochromes P450
Patrik Rydberg, Thomas Rod, Lars Olsen, Ulf Ryde
(2007) The Journal of Physical Chemistry Part B, 111 p.5445-5457
Journal articleThe role of axial ligands for the structure and function of chlorophylls
Jimmy Heimdal, Kasper Jensen, Ajitha Devarajan, Ulf Ryde
(2007) Journal of Biological Inorganic Chemistry, 12 p.49-61
Journal articleAccurate metal-site structures in proteins obtained by combining experimental data and quantum chemistry
Ulf Ryde
(2007) Dalton Transactions , p.607-625
Journal article reviewIdentification of the peroxy adduct in multicopper oxidases by a combination of computational chemistry and extended X-ray absorption fine-structure measurements
Ulf Ryde, Ya-Wen Hsiao, Lubomir Rulisek, Edward I. Solomon
(2007) Journal of the American Chemical Society, 129 p.726-727
Journal articlePerformance of density functionals for first row transition metal systems
Kasper Jensen, Björn Roos, Ulf Ryde
(2007) Journal of Chemical Physics, 126
Journal articleStructural insights into the active-ready form of [FeFe]-Hydrogenase and mechanistic details of its inhibition by carbon monoxide
Claudio Greco, Maurizio Bruschi, Jimmy Heimdal, Piercarlo Fantucci, Luca De Gioia, et al.
(2007) Inorganic Chemistry, 46 p.7256-7258
Journal articleA QM/MM investigation of the activation and catalytic mechanism of Fe-only hydrogenases
Claudio Greco, Maurizio Bruschi, Luca De Gioia, Ulf Ryde
(2007) Inorganic Chemistry, 46 p.5911-5921
Journal articlePrediction and rationalization of the pH dependence of the activity and stability of family 11 xylanases
Jacob Kongsted, Ulf Ryde, James Wydra, Jan H. Jensen
(2007) Biochemistry, 46 p.13581-13592
Journal articlePrediction of activation energies for hydrogen abstraction by cytochrome P450
Lars Olsen, Patrik Rydberg, Thomas H. Rod, Ulf Ryde
(2006) Journal of Medicinal Chemistry, 49 p.6489-6499
Journal articleLigand affinities predicted with the MM/PBSA method: Dependence on the simulation method and the force field
Aaron Weis, Kambiz Katebzadeh, Pär Söderhjelm, Ingemar Nilsson, Ulf Ryde
(2006) Journal of Medicinal Chemistry, 49 p.6596-6606
Journal articleMultireference ab initio calculations on reaction intermediates of the multicopper oxidases
Jakub Chalupsky, Frank Neese, Edward I. Solomon, Ulf Ryde, Lubomir Rulisek
(2006) Inorganic Chemistry, 45 p.11051-11059
Journal articleImplicit versus explicit solvent in free energy calculations of enzyme catalysis: Methyl transfer catalyzed by catechol O-methyltransferase
Thomas Rod, Patrik Rydberg, Ulf Ryde
(2006) Journal of Chemical Physics, 124
Journal articleComparison of overlap-based models for approximating the exchange-repulsion energy
Pär Söderhjelm, Gunnar Karlström, Ulf Ryde
(2006) Journal of Chemical Physics, 124
Journal articleThe reaction mechanism of iron and manganese superoxide dismutases studied by theoretical calculations
Lubomir Rulisek, Kasper Jensen, Kristoffer Lundgren, Ulf Ryde
(2006) Journal of Computational Chemistry, 27 p.1398-1414
Journal articleThe structures of frataxin oligomers reveal the mechanism for the delivery and detoxification of iron
Tobias Karlberg, Ulrika Schagerlöf, Oleksandr Gakh, Sungjo Park, Ulf Ryde, et al.
(2006) Structure, 14 p.1535-1546
Journal articleEXAFS structure refinement supplemented by computational chemistry
Ya-Wen Hsiao, Ye Tao, Jacob E. Shokes, Robert A. Scott, Ulf Ryde
(2006) Physical Review B (Condensed Matter and Materials Physics), 74
Journal articleInterpretation of EXAFS spectra for sitting-atop complexes with the help of computational methods
Ya-Wen Hsiao, Ulf Ryde
(2006) Inorganica Chimica Acta, 359 p.1081-1092
Journal articleStructural and photoluminescence properties of excited state intramolecular proton transfer capable compounds - Potential emissive and electron transport materials
Alexander Gaenko, Ajitha Devarajan, IV Tselinskii, Ulf Ryde
(2006) The Journal of Physical Chemistry Part A: Molecules, Spectroscopy, Kinetics, Environment and General Theory, 110 p.7935-7942
Journal articleStructure of reduced and oxidized manganese superoxide dismutase: A combined computational and experimental approach
Lubomir Rulisek, Ulf Ryde
(2006) The Journal of Physical Chemistry Part B, 110 p.11511-11518
Journal articleStructures of the high-valent metal-ion haem-oxygen intermediates in peroxidases, oxygenases and catalases
HP Hersleth, Ulf Ryde, Patrik Rydberg, CH Gorbitz, KK Andersson
(2006) Journal of Inorganic Biochemistry, 100 p.460-476
Journal article reviewCombined computational and crystallographic study of the oxidised states of [NiFe] hydrogenase
Pär Söderhjelm, Ulf Ryde
(2006) Journal of molecular structure. Theochem, 770 p.199-219
Journal articleHow the Co-C bond is cleaved in coenzyme B-12 enzymes: A theoretical study
Kasper Jensen, Ulf Ryde
(2005) Journal of the American Chemical Society, 127 p.9117-9128
Journal articleTheoretical study of structure of catalytic copper site in nitrite reductase
Niklas Källrot, Kristina Nilsson, Torben Rasmussen, Ulf Ryde
(2005) International Journal of Quantum Chemistry, 102 p.520-541
Journal articleNMR structure determination of proteins supplemented by quantum chemical calculations: Detailed structure of the Ca2+ sites in the EGF34 fragment of protein S
Ya-Wen Hsiao, Torbjörn Drakenberg, Ulf Ryde
(2005) Journal of Biomolecular NMR, 31 p.97-114
Journal articleAccurate QM/MM free energy calculations of enzyme reactions: Methylation by catechol O-methyltransferase
Thomas Rod, Ulf Ryde
(2005) Journal of Chemical Theory and Computation, 1 p.1240-1251
Journal articleComparison of chemical properties of iron, cobalt, and nickel porphyrins, corrins, and hydrocorphins
Kasper Jensen, Ulf Ryde
(2005) Journal of Porphyrins and Phthalocyanines, 9 p.581-606
Journal articleA combined quantum and molecular mechanical study of the O-2 reductive cleavage in the catalytic cycle of multicopper oxidases
Lubomir Rulisek, E I Solomon, Ulf Ryde
(2005) Inorganic Chemistry, 44 p.5612-5628
Journal articleA comparative reactivity study of microperoxidases based on hemin, mesohemin and deuterohemin
Ekaterina Ryabova, Patrik Rydberg, M Kolberg, E Harbitz, A L Barra, et al.
(2005) Journal of Inorganic Biochemistry, 99 p.852-863
Journal articleO2-binding to heme: electronic structure and spectrum of oxyheme, studied by multiconfigurational methods
Kasper Jensen, Björn Roos, Ulf Ryde
(2005) Journal of Inorganic Biochemistry, 99 p.45-54
Journal articleReaction mechanism of porphyrin metallation studied by theoretical methods
Yong Shen, Ulf Ryde
(2005) Chemistry: A European Journal, 11 p.1549-1564
Journal articleQuantum mechanical free energy barrier for an enzymatic reaction
Thomas Rod, Ulf Ryde
(2005) Physical Review Letters, 94 p.1-138302
Journal articleThe protonation status of compound II in myoglobin, studied by a combination of experimental data and quantum chemical calculations: Quantum refinement
Kristina Nilsson, H P Hersleth, Thomas Rod, K K Andersson, Ulf Ryde
(2004) Biophysical Journal, 87 p.3437-3447
Journal articleHow O-2 binds to heme - Reasons for rapid binding and spin inversion
Kasper Jensen, Ulf Ryde
(2004) Journal of Biological Chemistry, 279 p.14561-14569
Journal articleOn the role of the axial ligand in heme proteins: a theoretical study
Patrik Rydberg, Emma Sigfridsson, Ulf Ryde
(2004) Journal of Biological Inorganic Chemistry, 9 p.203-223
Journal articleProtonation status of metal-bound ligands can be determined by quantum refinement
Kristina Nilsson, Ulf Ryde
(2004) Journal of Inorganic Biochemistry, 98 p.1539-1546
Journal articleThe structure of sitting-atop complexes of metalloporphyrins studied by theoretical methods
Yong Shen, Ulf Ryde
(2004) Journal of Inorganic Biochemistry, 98 p.878-895
Journal articleBinding of benzylpenicillin to metallo-beta-lactamase: A QM/MM study
L Olsen, Torben Rasmussen, L Hemmingsen, Ulf Ryde
(2004) The Journal of Physical Chemistry Part B, 108 p.17639-17648
Journal articleTheoretical prediction of the co-c bond strength in cobalamins.
Kasper Jensen, Ulf Ryde
(2003) The Journal of Physical Chemistry Part A: Molecules, Spectroscopy, Kinetics, Environment and General Theory, 107 p.7539-7545
Journal articleImportance of proximal hydrogen bonds in haem proteins.
Kasper Jensen, Ulf Ryde
(2003) Molecular Physics, 101 p.2003-2018
Journal articleMetal binding to Bacillus subtilis ferrochelatase and interaction between metal sites.
David Lecerof, Michel Fodje, Román Alvarez León, Ulf Olsson, Andreas Hansson, et al.
(2003) Journal of Biological Inorganic Chemistry, 8 p.452-458
Journal articleMetal ion enhanced binding of amd3100 to asp-262 in the cxcr4 receptor.
L O Gerlach, J S Jacobsen, Kasper Jensen, M R Rosenkilde, R T Skerlj, et al.
(2003) Biochemistry, 42 p.710-717
Journal articleThe importance of porphyrin distortions for the ferrochelatase reaction.
Emma Sigfridsson, Ulf Ryde
(2003) Journal of Biological Inorganic Chemistry, 8 p.273-282
Journal articleCombined quantum and molecular mechanics calculations on metalloproteins.
Ulf Ryde
(2003) Current Opinion in Chemical Biology, 7 p.136-142
Journal article reviewQuantum refinement - a combination of quantum chemistry and protein crystallography.
Ulf Ryde, Kristina Nilsson
(2003) Journal of molecular structure. Theochem, 632 p.259-275
Journal article reviewLactam hydrolysis catalyzed by mononuclear metallo-beta-lactamases: A density functional study
L Olsen, J Antony, Ulf Ryde, H-W Adolph, L Hemmingsen
(2003) The Journal of Physical Chemistry Part B, 107 p.2366-2375
Journal articleMolecular orbital theory.
Björn Roos, Ulf Ryde
(2003) Comprehensive Coordination Chemistry 2 (Vol. 1)
Book chapterComparison of the chemical properties of iron and cobalt porphyrins and corrins.
Kasper Jensen, Ulf Ryde
(2003) ChemBioChem, 4 p.413-424
Journal articleQuantum Chemistry Can Locally Improve Protein Crystal Structures
Ulf Ryde, Kristina Nilsson
(2003) Journal of the American Chemical Society, 125 p.14232-14233
Journal articleMolcas: a program package for computational chemistry.
Gunnar Karlström, Roland Lindh, Per-Åke Malmqvist, Björn Roos, Ulf Ryde, et al.
(2003) Computational Materials Science, 28 p.222-239
Journal articleAn automatic method to generate force-field parameters for hetero-compounds.
Kristina Nilsson, David Lecerof, Emma Sigfridsson, Ulf Ryde
(2003) Acta Crystallographica. Section D: Biological Crystallography, 59 p.274-289
Journal articleConversion of homocysteine to methionine by methionine synthase: a density functional study.
Kasper Jensen, Ulf Ryde
(2003) Journal of the American Chemical Society, 125 p.13970-13971
Journal articleOn the role of covalent strain in protein function
Ulf Ryde
(2002) Recent research developments in protein engineering, Vol. 2 , p.65-91
Book chapterTheoretical study of the discrimination between O(2) and CO by myoglobin.
Emma Sigfridsson, Ulf Ryde
(2002) Journal of Inorganic Biochemistry, 91 p.101-115
Journal articleThe axial N-base has minor influence on Co-C bond cleavage in cobalamins
Kasper Jensen, Ulf Ryde
(2002) Journal of molecular structure. Theochem, 585 p.239-255
Journal articleRestrained point-charge models for disaccharides
E Sigfridsson, Ulf Ryde, BL Bush
(2002) Journal of Computational Chemistry, 23 p.351-364
Journal articleQuantum chemical geometry optimizations in proteins using crystallographic raw data.
Ulf Ryde, Lars Olsen, Kristina Nilsson
(2002) Journal of Computational Chemistry, 23 p.1058-1070
Journal articleGeometry, Reduction Potential, and Reorganization Energy of the Binuclear CuA Site, Studied by Density Functional Theory
Mats H. M. Olsson, Ulf Ryde
(2001) Journal of the American Chemical Society, 123 p.7866-7876
Journal articleA theoretical study of the copper–cysteine bond in blue copper proteins
Ulf Ryde, Mats H. M. Olsson, Björn Roos, Antonio Borin-Carlos
(2001) Theoretical Chemistry Accounts, 105 p.452-462
Journal articleInner-sphere reorganization energy of iron-sulfur clusters studied with theoretical methods
Emma Sigfridsson, Mats H. M. Olsson, Ulf Ryde
(2001) Inorganic Chemistry, 40 p.2509-2519
Journal articleStructure, strain, and reorganization energy of blue copper models in the protein
Ulf Ryde, Mats H. M. Olsson
(2001) International Journal of Quantum Chemistry, 81 p.335-347
Journal articleA comparison of the inner-sphere reorganization energies of cytochromes, iron-sulphur clusters, and blue copper proteins
Emma Sigfridsson, Mats H. M. Olsson, Ulf Ryde
(2001) The Journal of Physical Chemistry Part B, 105 p.5546-5552
Journal articleThe structure and function of blue copper proteins
Ulf Ryde, Mats H M Olsson, Kristine Pierloot
(2001) Theoretical and Computational Chemistry, 9 p.1-55
Journal article reviewOn the role of strain in blue copper proteins
Ulf Ryde, Mats H M Olsson, Björn O. Roos, Jan O A De Kerpel, Kristine Pierloot
(2000) Journal of Biological Inorganic Chemistry, 5 p.565-574
Journal articleCarboxylate binding modes in zinc proteins : A theoretical study
Ulf Ryde
(1999) Biophysical Journal, 77 p.2777-2787
Journal articleThe influence of axial ligands on the reduction potential of blue copper proteins
Mats H M Olsson, Ulf Ryde
(1999) Journal of Biological Inorganic Chemistry, 4 p.654-663
Journal articleRedesign of the coenzyme specificity in L-lactate dehydrogenase from bacillus stearothermophilus using site-directed mutagenesis and media engineering
Niklas Holmberg, U Ryde, L Bülow
(1999) Protein Engineering, 12 p.6-851
Journal articleGeometric and Electronic Structure of Co(II)-Substituted Azurin
Jan O A De Kerpel, Kristine Pierloot, Ulf Ryde
(1999) The Journal of Physical Chemistry Part B, 103 p.8375-8382
Journal articleProtein strain in blue copper proteins studied by free energy perturbations
Jan O A De Kerpel, Ulf Ryde
(1999) Proteins: Structure, Function and Genetics, 36 p.157-174
Journal articleNuclear quadrupole interactions in cadmium complexes : Semiempirical and ab initio calculations
Lars Hemmingsen, Ulf Ryde, Rogert Bauer
(1999) Zeitschrift fur Naturforschung - Section A Journal of Physical Sciences, 54 p.422-430
Journal articleOn the significance of hydrogen bonds for the discrimination between CO and O2 by myoglobin
Emma Sigfridsson, Ulf Ryde
(1999) Journal of Biological Inorganic Chemistry, 4 p.99-110
Journal articleProteins, Blue Copper: Electronic Spectra
Ulf Ryde, Mats H. M. Olsson, Björn O. Roos, Kristine Pierloot, Jan O. A. De Kerpel
(1998) The Encyclopaedia of Computational Chemistry , p.2255-2270
Book chapterRelation between the structure and spectroscopic properties of blue copper proteins
Kristine Pierloot, Jan O A De Kerpel, Ulf Ryde, Mats H M Olsson, Björn O. Roos
(1998) Journal of the American Chemical Society, 120 p.13156-13166
Journal articleQuantum chemical calculations of the reorganization energy of blue- copper proteins
Mats H M Olsson, Ulf Ryde, Björn O. Roos
(1998) Protein Science, 7 p.2659-2668
Journal articleTheoretical study of the structural and spectroscopic properties of stellacyanin
Jan O A De Kerpel, Kristine Pierloot, Ulf Ryde, Björn O. Roos
(1998) The Journal of Physical Chemistry Part B, 102 p.4638-4647
Journal articleOn the relative stability of tetragonal and trigonal Cu(II) complexes with relevance to the blue copper proteins
Mats H M Olsson, Ulf Ryde, Björn O. Roos, Kristine Pierloot
(1998) Journal of Biological Inorganic Chemistry, 3 p.109-125
Journal articleComparison of methods for deriving atomic charges from the electrostatic potential and moments
Emma Sigfridsson, Ulf Ryde
(1998) Journal of Computational Chemistry, 19 p.377-395
Journal article reviewOn the significance of the trigger reaction in the action of the calicheamicin γI1 anti-cancer drug
Roland Lindh, Ulf Ryde, Martin Schütz
(1997) Theoretical Chemistry Accounts, 97 p.203-210
Journal articleThe active-site metal coordination geometry of cadmium-substituted alcohol dehydrogenase : A theoretical interpretation of perturbed angular correlation of γ-ray measurements
U. Ryde, L. Hemmingsen
(1997) Journal of Biological Inorganic Chemistry, 2 p.567-579
Journal articleTheoretical study of the electronic spectrum of plastocyanin
Kristine Pierloot, Jan O A De Kerpel, Ulf Ryde, Björn O. Roos
(1997) Journal of the American Chemical Society, 119 p.218-226
Journal articleThe cupric geometry of blue copper proteins is not strained
Ulf Ryde, Mats H M Olsson, Kristine Pierloot, Björn O. Roos
(1996) Journal of Molecular Biology, 261 p.586-596
Journal articleThe coordination chemistry of the structural zinc ion in alcohol dehydrogenase studied by ab initio quantum chemical calculations
Ulf Ryde
(1996) European Biophysics Journal, 24 p.213-221
Journal articleAb initio calculations of electric field gradients in cadmium complexes
Lars Hemmingsen, Ulf Ryde
(1996) Journal of Physical Chemistry, 100 p.4803-4809
Journal articleThe coordination of the catalytic zinc ion in alcohol dehydrogenase studied by combined quantum-chemical and molecular mechanics calculations
Ulf Ryde
(1996) Journal of Computer-Aided Molecular Design, 10 p.153-164
Journal articleOn the role of Glu‐68 in alcohol dehydrogenase
Ulf Ryde
(1995) Protein Science, 4 p.1124-1132
Journal articleMolecular dynamics simulations of alcohol dehydrogenase with a four‐ or five‐coordinate catalytic zinc ion
Ulf Ryde
(1995) Proteins: Structure, Function and Genetics, 21 p.40-56
Journal articleThe coordination chemistry of the catalytic zinc ion in alcohol dehydrogenase studied by ab initio quantum chemical calculations
Ulf Ryde
(1994) International Journal of Quantum Chemistry, 52 p.1229-1243
Journal articleOscillations in coupled enzymic reactions at high concentration of enzyme
Ulf Ryde-Pettersson
(1992) BBA - Protein Structure and Molecular Enzymology, 1119 p.118-122
Journal articleIdentification of possible two‐reactant sources of oscillations in the Calvin photosynthesis cycle and ancillary pathways
Ulf Ryde-Pettersson
(1991) European Journal of Biochemistry, 198 p.613-619
Journal articleModel studies of the regulation of the Calvin photosynthesis cycle by cytosolic metabolites
Gösta Pettersson, Ulf Ryde-Pettersson
(1990) Biomedica Biochimica Acta, 49 p.723-732
Journal articleOn the mechanistic origin of damped oscillations in biochemical reaction systems
Ulf Ryde-Pettersson
(1990) European Journal of Biochemistry, 194 p.431-436
Journal articleMetabolites controlling the rate of starch synthesis in the chloroplast of C3 plants
Gösta Pettersson, Ulf Ryde
(1989) European Journal of Biochemistry, 179 p.169-172
Journal articleA theoretical treatment of damped oscillations in the transient state kinetics of single‐enzyme reactions
Ulf Ryde-Pettersson
(1989) European Journal of Biochemistry, 186 p.145-148
Journal articleOn the regulatory significance of inhibitors acting on non‐equilibrium enzymes in the Calvin photosynthesis cycle
Gösta Pettersson, Ulf Ryde-Pettersson
(1989) European Journal of Biochemistry, 182 p.373-377
Journal articleDependence of the Calvin cycle activity on kinetic parameters for the interaction of non‐equilibrium cycle enzymes with their substrates
Gösta Pettersson, Ulf Ryde-Pettersson
(1989) European Journal of Biochemistry, 186 p.683-687
Journal articleMechanism of glyceraldehyde‐3‐phosphate transfer from aldolase to glyceraldehyde‐3‐phosphate dehydrogenase
Jan Kvassman, Gösta Pettersson, Ulf Ryde-Pettersson
(1988) European Journal of Biochemistry, 172 p.427-431
Journal articleA mathematical model of the Calvin photosynthesis cycle
Gösta Pettersson, Ulf Ryde-Pettersson
(1988) European Journal of Biochemistry, 175 p.661-672
Journal articleEffects of metabolite binding to ribulosebisphosphate carboxylase on the activity of the Calvin photosynthesis cycle
Gösta Pettersson, Ulf Ryde-Pettersson
(1988) European Journal of Biochemistry, 177 p.351-355
Journal articleA rapid‐equilibrium model for the control of the Calvin photosynthesis cycle by cytosolic orthophosphate
Gösta Pettersson, Ulf Ryde-Pettersson
(1987) European Journal of Biochemistry, 169 p.423-429
Journal article
Research group member(s)
Links will open in Lund University’s Research Portal unless otherwise stated.
- Marcos Verissimo Alves, Postdoc
- Meiting Wang, Postdoc
- Hao Jiang, PhD student
- Kristoffer Lundgren, PhD student
- Victor Vysotskiy, PhD student (Lund University's website)
- Gayathri Yuvaraj, PhD student
- Xiaoli Sun (Jilin University, Institute of Theoretical Chemistry, China), Guest researcher
- Parisa Fereidounpour (Aalborg University, Denmark), Guest researcher
- Erik Hedegård (University of Southern Denmark), Guest researcher
Former employees (the last ten years)
- Vilhelm Ekberg (PhD student 2019-2023)
- Magne Torbjörnsson (PhD student 2018-2023)
- Justin Bergmann (PhD student 2018-2022), currently at ESS
- Lili Cao (PhD student 2016-2020); currently at AstraZeneca
- Dr. Octav Caldararu (PhD student 2015-2019), currently at Zealand Pharma.
- Dr. Majda Misini Ignjatovic (PhD student 2015-2019).
- Sonia Jafari (Guest PhD student (2018-2019)
- Dr. Meiting Wang (Guest PhD student (2018-2019), currently back in Lund.
- Dr. Geng Dong (PhD student 2014-2018).
- Dr. Fatemeh Alavi Sadat (Guest PhD student 2016).
- Dr. Casper Steinmann Svendssen (postdoc 2017), currently at Aalborg University.
- Dr. Erik Hedegård (Guest PhD student; Postdoc 2016-2017); currently at South Denmark University.
- Dr. Martin A. Olsson (PhD student 2014-2018).
- Francesco Manzoni (PhD student, 2013-2017), deseased in 2017.
- Dr. Paulius Mikulskis (PhD student 2011-2015); currently in Nottingham.