Ulf Ryde

Publication Activity (10 Years)

Years Active: 2016-2024
Publications (10 Years): 76

Top Topics

Crystal Structure

Hydrogen Peroxide

Molecular Dynamics

Top Venues

Inorganic chemistry

Physical chemistry chemical physics : PCCP

Journal of chemical theory and computation

Molecules (Basel, Switzerland)

This page only lists publications with an associated author ORCID identifier.

Publications

Anna Rovaletti, Giorgio Moro, Ugo Cosentino, Ulf Ryde, Claudio Greco
CO Oxidation Mechanism of Silver-Substituted Mo/Cu CO-Dehydrogenase - Analogies and Differences to the Native Enzyme. Chemphyschem : a European journal of chemical physics and physical chemistry 25 (13) (2024)
Hao Jiang, Ulf Ryde
Reaction Mechanism for CO Reduction by Mo-Nitrogenase Studied by QM/MM. Inorganic chemistry 63 (34) (2024)
Anna Rovaletti, Giorgio Moro, Ugo Cosentino, Ulf Ryde, Claudio Greco
CO Oxidation Mechanism of Silver-Substituted Mo/Cu CO-Dehydrogenase - Analogies and Differences to the Native Enzyme. Chemphyschem : a European journal of chemical physics and physical chemistry 25 (13) (2024)
Hao Jiang, Ulf Ryde
Reaction Mechanism for CO Reduction by Mo-Nitrogenase Studied by QM/MM. Inorganic chemistry 63 (34) (2024)
Hao Jiang, Ulf Ryde
Putative reaction mechanism of nitrogenase with a half-dissociated S2B ligand. Dalton transactions (Cambridge, England : 2003) 53 (27) (2024)
Anna Rovaletti, Giorgio Moro, Ugo Cosentino, Ulf Ryde, Claudio Greco
CO Oxidation Mechanism of Silver-Substituted Mo/Cu CO-Dehydrogenase - Analogies and Differences to the Native Enzyme. Chemphyschem : a European journal of chemical physics and physical chemistry (2024)
Victor P Vysotskiy, Claudia Filippi, Ulf Ryde
Scalar Relativistic All-Electron and Pseudopotential Ab Initio Study of a Minimal Nitrogenase [Fe(SH) 4 H] - Model Employing Coupled-Cluster and Auxiliary-Field Quantum Monte Carlo Many-Body Methods. The journal of physical chemistry. A (2024)
Hao Jiang, Ulf Ryde
Reaction Mechanism for CO Reduction by Mo-Nitrogenase Studied by QM/MM. Inorganic chemistry 63 (34) (2024)
Hao Jiang, Ulf Ryde
Putative reaction mechanism of nitrogenase with a half-dissociated S2B ligand. Dalton transactions (Cambridge, England : 2003) (2024)
Meiting Wang, Ye Mei, Ulf Ryde
Convergence criteria for single-step free-energy calculations: the relation between the Π bias measure and the sample variance. Chemical science 15 (23) (2024)
Meiting Wang, Baoyi Fan, Wenfeng Lu, Ulf Ryde, Yuxiao Chang, Di Han, Jiarui Lu, Taigang Liu, Qinghe Gao, Changpo Chen, Yongtao Xu
Unraveling the Binding Mode of Cyclic Adenosine-Inosine Monophosphate (cAIMP) to STING through Molecular Dynamics Simulations. Molecules (Basel, Switzerland) 29 (11) (2024)
Hao Jiang, Ulf Ryde
H 2 formation from the E 2 -E 4 states of nitrogenase. Physical chemistry chemical physics : PCCP 26 (2) (2024)
Meiting Wang, Ye Mei, Ulf Ryde
Convergence criteria for single-step free-energy calculations: the relation between the Π bias measure and the sample variance. Chemical science 15 (23) (2024)
Meiting Wang, Baoyi Fan, Wenfeng Lu, Ulf Ryde, Yuxiao Chang, Di Han, Jiarui Lu, Taigang Liu, Qinghe Gao, Changpo Chen, Yongtao Xu
Unraveling the Binding Mode of Cyclic Adenosine-Inosine Monophosphate (cAIMP) to STING through Molecular Dynamics Simulations. Molecules (Basel, Switzerland) 29 (11) (2024)
Victor P Vysotskiy, Claudia Filippi, Ulf Ryde
Scalar Relativistic All-Electron and Pseudopotential Ab Initio Study of a Minimal Nitrogenase [Fe(SH) 4 H] - Model Employing Coupled-Cluster and Auxiliary-Field Quantum Monte Carlo Many-Body Methods. The journal of physical chemistry. A 128 (7) (2024)
Hao Jiang, Ulf Ryde
H 2 formation from the E 2 -E 4 states of nitrogenase. Physical chemistry chemical physics : PCCP 26 (2) (2024)
Victor P Vysotskiy, Claudia Filippi, Ulf Ryde
Scalar Relativistic All-Electron and Pseudopotential Ab Initio Study of a Minimal Nitrogenase [Fe(SH) 4 H] - Model Employing Coupled-Cluster and Auxiliary-Field Quantum Monte Carlo Many-Body Methods. The journal of physical chemistry. A 128 (7) (2024)
Hao Jiang, Ulf Ryde
Reaction Mechanism for CO Reduction by Mo-Nitrogenase Studied by QM/MM. Inorganic chemistry (2024)
Victor P Vysotskiy, Claudia Filippi, Ulf Ryde
Scalar Relativistic All-Electron and Pseudopotential Ab Initio Study of a Minimal Nitrogenase [Fe(SH) 4 H] - Model Employing Coupled-Cluster and Auxiliary-Field Quantum Monte Carlo Many-Body Methods. The journal of physical chemistry. A 128 (7) (2024)
Anna Rovaletti, Giorgio Moro, Ugo Cosentino, Ulf Ryde, Claudio Greco
CO Oxidation Mechanism of Silver-Substituted Mo/Cu CO-Dehydrogenase - Analogies and Differences to the Native Enzyme. Chemphyschem : a European journal of chemical physics and physical chemistry 25 (13) (2024)
Meiting Wang, Baoyi Fan, Wenfeng Lu, Ulf Ryde, Yuxiao Chang, Di Han, Jiarui Lu, Taigang Liu, Qinghe Gao, Changpo Chen, Yongtao Xu
Unraveling the Binding Mode of Cyclic Adenosine-Inosine Monophosphate (cAIMP) to STING through Molecular Dynamics Simulations. Molecules (Basel, Switzerland) 29 (11) (2024)
Wijitra Meelua, Tanchanok Wanjai, Natechanok Thinkumrob, Julianna Oláh, James R Ketudat Cairns, Supa Hannongbua, Ulf Ryde, Jitrayut Jitonnom
A computational study of the reaction mechanism and stereospecificity of dihydropyrimidinase. Physical chemistry chemical physics : PCCP 25 (12) (2023)
Wijitra Meelua, Tanchanok Wanjai, Natechanok Thinkumrob, Julianna Oláh, James R Ketudat Cairns, Supa Hannongbua, Ulf Ryde, Jitrayut Jitonnom
A computational study of the reaction mechanism and stereospecificity of dihydropyrimidinase. Physical chemistry chemical physics : PCCP 25 (12) (2023)
Hao Jiang, Kristoffer J M Lundgren, Ulf Ryde
Protonation of Homocitrate and the E 1 State of Fe-Nitrogenase Studied by QM/MM Calculations. Inorganic chemistry (2023)
Wijitra Meelua, Tanchanok Wanjai, Natechanok Thinkumrob, Julianna Oláh, James R Ketudat Cairns, Supa Hannongbua, Ulf Ryde, Jitrayut Jitonnom
A computational study of the reaction mechanism and stereospecificity of dihydropyrimidinase. Physical chemistry chemical physics : PCCP (2023)
Hao Jiang, Ulf Ryde
H 2 formation from the E 2 -E 4 states of nitrogenase. Physical chemistry chemical physics : PCCP (2023)
Hao Jiang, Ulf Ryde
N 2 binding to the E 0 -E 4 states of nitrogenase. Dalton transactions (Cambridge, England : 2003) (2023)
Wijitra Meelua, Tanchanok Wanjai, Natechanok Thinkumrob, Julianna Oláh, James R Ketudat Cairns, Supa Hannongbua, Ulf Ryde, Jitrayut Jitonnom
A computational study of the reaction mechanism and stereospecificity of dihydropyrimidinase. Physical chemistry chemical physics : PCCP 25 (12) (2023)
Huanchen Zhai, Seunghoon Lee, Zhi-Hao Cui, Lili Cao, Ulf Ryde, Garnet Kin-Lic Chan
Multireference Protonation Energetics of a Dimeric Model of Nitrogenase Iron-Sulfur Clusters. The journal of physical chemistry. A (2023)
Javad Shirazi, Sonia Jafari, Ulf Ryde, Mehdi Irani
Catalytic Reaction Mechanism of Glyoxalase II: A Quantum Mechanics/Molecular Mechanics Study. The journal of physical chemistry. B (2023)
Hao Jiang, Oskar K G Svensson, Ulf Ryde
Quantum Mechanical Calculations of Redox Potentials of the Metal Clusters in Nitrogenase. Molecules (Basel, Switzerland) 28 (1) (2022)
Sonia Jafari, Yakini A Tavares Santos, Justin Bergmann, Mehdi Irani, Ulf Ryde
Benchmark Study of Redox Potential Calculations for Iron-Sulfur Clusters in Proteins. Inorganic chemistry 61 (16) (2022)
Anna Rovaletti, Ulf Ryde, Giorgio Moro, Ugo Cosentino, Claudio Greco
How general is the effect of the bulkiness of organic ligands on the basicity of metal-organic catalysts? H 2 -evolving Mo oxides/sulphides as case studies. Physical chemistry chemical physics : PCCP (2022)
Anna Rovaletti, Giorgio Moro, Ugo Cosentino, Ulf Ryde, Claudio Greco
Can Water Act as a Nucleophile in CO Oxidation Catalysed by Mo/Cu CO-Dehydrogenase? Answers from Theory. Chemphyschem : a European journal of chemical physics and physical chemistry 23 (8) (2022)
Hao Jiang, Ulf Ryde
Thermodynamically Favourable States in the Reaction of Nitrogenase without Dissociation of any Sulfide Ligand. Chemistry (Weinheim an der Bergstrasse, Germany) 28 (14) (2022)
Hao Jiang, Oskar K G Svensson, Ulf Ryde
QM/MM Study of Partial Dissociation of S2B for the E 2 Intermediate of Nitrogenase. Inorganic chemistry 61 (45) (2022)
Hao Jiang, Oskar K G Svensson, Ulf Ryde
Quantum Mechanical Calculations of Redox Potentials of the Metal Clusters in Nitrogenase. Molecules (Basel, Switzerland) 28 (1) (2022)
Hao Jiang, Oskar K G Svensson, Ulf Ryde
Quantum Mechanical Calculations of Redox Potentials of the Metal Clusters in Nitrogenase. Molecules (Basel, Switzerland) 28 (1) (2022)
Hao Jiang, Oskar K G Svensson, Lili Cao, Ulf Ryde
Proton Transfer Pathways in Nitrogenase with and without Dissociated S2B. Angewandte Chemie (International ed. in English) 61 (39) (2022)
Vilhelm Ekberg, Marley L Samways, Majda Misini Ignjatović, Jonathan W Essex, Ulf Ryde
Comparison of Grand Canonical and Conventional Molecular Dynamics Simulation Methods for Protein-Bound Water Networks. ACS Physical Chemistry Au 2 (3) (2022)
Sonia Jafari, Ulf Ryde, Mehdi Irani
QM/MM Study of the Catalytic Reaction of Myrosinase; Importance of Assigning Proper Protonation States of Active-Site Residues. Journal of chemical theory and computation 17 (3) (2021)
Vinardas Kelpšas, Octav Caldararu, Matthew P Blakeley, Nicolas Coquelle, Rikkert K Wierenga, Ulf Ryde, Claes von Wachenfeldt, Esko Oksanen
Neutron structures of Leishmania mexicana triosephosphate isomerase in complex with reaction-intermediate mimics shed light on the proton-shuttling steps. IUCrJ 8 (Pt 4) (2021)
Vilhelm Ekberg, Ulf Ryde
On the Use of Interaction Entropy and Related Methods to Estimate Binding Entropies. Journal of chemical theory and computation 17 (8) (2021)
Octav Caldararu, Vilhelm Ekberg, Derek T Logan, Esko Oksanen, Ulf Ryde
Exploring ligand dynamics in protein crystal structures with ensemble refinement. Acta crystallographica. Section D, Structural biology 77 (Pt 8) (2021)
Johan Wallerstein, Vilhelm Ekberg, Majda Misini Ignjatović, Rohit Kumar, Octav Caldararu, Kristoffer Peterson, Sven Wernersson, Ulrika Brath, Hakon Leffler, Esko Oksanen, Derek T Logan, Ulf J Nilsson, Ulf Ryde, Mikael Akke
Entropy-Entropy Compensation between the Protein, Ligand, and Solvent Degrees of Freedom Fine-Tunes Affinity in Ligand Binding to Galectin-3C. JACS Au 1 (4) (2021)
Anna Rovaletti, Claudio Greco, Ulf Ryde
QM/MM study of the binding of H2 to MoCu CO dehydrogenase: development and applications of improved H2 van der Waals parameters. Journal of molecular modeling 27 (3) (2021)
Lili Cao, Ulf Ryde
What Is the Structure of the E4 Intermediate in Nitrogenase? Journal of chemical theory and computation 16 (3) (2020)
Sonia Jafari, Ulf Ryde, Adam Emad Ahmed Fouda, Fatemeh Sadat Alavi, Geng Dong, Mehdi Irani
Quantum Mechanics/Molecular Mechanics Study of the Reaction Mechanism of Glyoxalase I. Inorganic chemistry 59 (4) (2020)
Sonia Jafari, Ulf Ryde, Mehdi Irani
Two-Substrate Glyoxalase I Mechanism: A Quantum Mechanics/Molecular Mechanics Study. Inorganic chemistry 60 (1) (2020)
Octav Caldararu, Majda Misini Ignjatović, Esko Oksanen, Ulf Ryde
Water structure in solution and crystal molecular dynamics simulations compared to protein crystal structures. RSC advances 10 (14) (2020)
Lili Cao, Melanie C Börner, Justin Bergmann, Octav Caldararu, Ulf Ryde
Geometry and Electronic Structure of the P-Cluster in Nitrogenase Studied by Combined Quantum Mechanical and Molecular Mechanical Calculations and Quantum Refinement. Inorganic chemistry 58 (15) (2019)
Meiting Wang, Ye Mei, Ulf Ryde
Host-Guest Relative Binding Affinities at Density-Functional Theory Level from Semiempirical Molecular Dynamics Simulations. Journal of chemical theory and computation 15 (4) (2019)
Maria Luisa Verteramo, Olof Stenström, Majda Misini Ignjatović, Octav Caldararu, Martin A Olsson, Francesco Manzoni, Hakon Leffler, Esko Oksanen, Derek T Logan, Ulf J Nilsson, Ulf Ryde, Mikael Akke
Interplay between Conformational Entropy and Solvation Entropy in Protein-Ligand Binding. Journal of the American Chemical Society 141 (5) (2019)
Rohit Kumar, Majda Misini Ignjatović, Kristoffer Peterson, Martin Olsson, Hakon Leffler, Ulf Ryde, Ulf J Nilsson, Derek T Logan
Structure and Energetics of Ligand-Fluorine Interactions with Galectin-3 Backbone and Side-Chain Amides: Insight into Solvation Effects and Multipolar Interactions. ChemMedChem 14 (16) (2019)
Adrian M V Brânzanic, Ulf Ryde, Radu Silaghi Dumitrescu
Why does sulfite reductase employ siroheme? Chemical communications (Cambridge, England) 55 (93) (2019)
Casper Steinmann, Martin A Olsson, Ulf Ryde
Relative Ligand-Binding Free Energies Calculated from Multiple Short QM/MM MD Simulations. Journal of chemical theory and computation 14 (6) (2018)
Geng Dong, Ulf Ryde, Hans Jørgen Aagaard Jensen, Erik Donovan Hedegård
Exploration of H2 binding to the [NiFe]-hydrogenase active site with multiconfigurational density functional theory. Physical chemistry chemical physics : PCCP 20 (2) (2018)
Octav Caldararu, Milica Feldt, Daniela Cioloboc, Marie-Céline van Severen, Kerstin Starke, Ricardo A Mata, Ebbe Nordlander, Ulf Ryde
QM/MM study of the reaction mechanism of sulfite oxidase. Scientific reports 8 (1) (2018)
Sonia Jafari, Nadia Kazemi, Ulf Ryde, Mehdi Irani
Higher Flexibility of Glu-172 Explains the Unusual Stereospecificity of Glyoxalase I. Inorganic chemistry 57 (9) (2018)
Francesco Manzoni, Ulf Ryde
Assessing the stability of free-energy perturbation calculations by performing variations in the method. Journal of computer-aided molecular design 32 (4) (2018)
Octav Caldararu, Esko Oksanen, Ulf Ryde, Erik Donovan Hedegård
Mechanism of hydrogen peroxide formation by lytic polysaccharide monooxygenase. Chemical science 10 (2) (2018)
Meiting Wang, Ye Mei, Ulf Ryde
Predicting Relative Binding Affinity Using Nonequilibrium QM/MM Simulations. Journal of chemical theory and computation 14 (12) (2018)
Erik Donovan Hedegård, Ulf Ryde
Molecular mechanism of lytic polysaccharide monooxygenases. Chemical science 9 (15) (2018)
Lili Cao, Octav Caldararu, Ulf Ryde
Protonation and Reduction of the FeMo Cluster in Nitrogenase Studied by Quantum Mechanics/Molecular Mechanics (QM/MM) Calculations. Journal of chemical theory and computation 14 (12) (2018)
Geng Dong, Quan Manh Phung, Kristine Pierloot, Ulf Ryde
Reaction Mechanism of [NiFe] Hydrogenase Studied by Computational Methods. Inorganic chemistry 57 (24) (2018)
Octav Caldararu, Martin A Olsson, Majda Misini Ignjatović, Meiting Wang, Ulf Ryde
Binding free energies in the SAMPL6 octa-acid host-guest challenge calculated with MM and QM methods. Journal of computer-aided molecular design 32 (10) (2018)
Lili Cao, Octav Caldararu, Ulf Ryde
Protonation States of Homocitrate and Nearby Residues in Nitrogenase Studied by Computational Methods and Quantum Refinement. The journal of physical chemistry. B 121 (35) (2017)
Martin A Olsson, Alfonso T García-Sosa, Ulf Ryde
Binding affinities of the farnesoid X receptor in the D3R Grand Challenge 2 estimated by free-energy perturbation and docking. Journal of computer-aided molecular design 32 (1) (2017)
Majda Misini Ignjatović, Paulius Mikulskis, Pär Söderhjelm, Ulf Ryde
Can MM/GBSA calculations be sped up by system truncation? Journal of computational chemistry 39 (7) (2017)
Lili Cao, Octav Caldararu, Amy C Rosenzweig, Ulf Ryde
Quantum Refinement Does Not Support Dinuclear Copper Sites in Crystal Structures of Particulate Methane Monooxygenase. Angewandte Chemie (International ed. in English) 57 (1) (2017)
Ulf Ryde
How Many Conformations Need To Be Sampled To Obtain Converged QM/MM Energies? The Curse of Exponential Averaging. Journal of chemical theory and computation 13 (11) (2017)
Francesco Manzoni, Jon Uranga, Samuel Genheden, Ulf Ryde
Can System Truncation Speed up Ligand-Binding Calculations with Periodic Free-Energy Simulations? Journal of chemical information and modeling 57 (11) (2017)
Martin A Olsson, Ulf Ryde
Comparison of QM/MM Methods To Obtain Ligand-Binding Free Energies. Journal of chemical theory and computation 13 (5) (2017)
Fatemeh Sadat Alavi, Mansour Zahedi, Nasser Safari, Ulf Ryde
QM/MM Study of the Conversion of Oxophlorin into Verdoheme by Heme Oxygenase. The journal of physical chemistry. B 121 (51) (2017)
Majda Misini Ignjatović, Octav Caldararu, Geng Dong, Camila Muñoz-Gutierrez, Francisco Adasme-Carreño, Ulf Ryde
Binding-affinity predictions of HSP90 in the D3R Grand Challenge 2015 with docking, MM/GBSA, QM/MM, and free-energy simulations. Journal of computer-aided molecular design 30 (9) (2016)
Octav Caldararu, Martin A Olsson, Christoph Riplinger, Frank Neese, Ulf Ryde
Binding free energies in the SAMPL5 octa-acid host-guest challenge calculated with DFT-D3 and CCSD(T). Journal of computer-aided molecular design 31 (1) (2016)