Ulf Ryde

发表

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.

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.

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.

Restrained point‐charge models for disaccharides

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

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.

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

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

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

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

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.

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..

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

Ulf Ryde, Martin A. Olsson, Majda Misini Ignjatović, 2018, Journal of Computer-Aided Molecular Design.

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..

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

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

How to obtain statistically converged MM/GBSA results

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

Conformational dependence of charges in protein simulations

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

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

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

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

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

Quantum chemical geometry optimizations in proteins using crystallographic raw data

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

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..

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..

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

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

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.

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

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

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

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

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

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

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

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

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..

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

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

Estimates of ligand-binding affinities supported by quantum mechanical methods

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

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

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

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

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

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.

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.

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.

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.

Ligand Affinities Estimated by Quantum Chemical Calculations.

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

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.

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

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

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.

Combined quantum and molecular mechanics calculations on metalloproteins.

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

Quantum refinement — a method to determine protonation and oxidation states of metal sites in protein crystal structures

Kristina Nilsson, Ulf Ryde, 2003 .

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.

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

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

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.

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.

Nonpolar Solvation Free Energies of Protein-Ligand Complexes.

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

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.

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.

On the Convergence of QM/MM Energies.

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

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

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

On the role of strain in blue copper proteins

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

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

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

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

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

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

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

Cobalamins uncovered by modern electronic structure calculations

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

Quantum chemistry can locally improve protein crystal structures.

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

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.

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

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

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

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

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

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

Relation between the Structure and Spectroscopic Properties of Blue Copper Proteins

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

Quantum-mechanical studies of reactions performed by cytochrome P450 enzymes

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

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

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

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.

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.

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

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

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.

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

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

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.

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

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

Accuracy of typical approximations in classical models of intermolecular polarization.

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

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.

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

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

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

Ulf Ryde, U. Ryde, 1994 .

Prediction of activation energies for aromatic oxidation by cytochrome P450.

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

How O2 Binds to Heme

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

Prediction of activation energies for hydrogen abstraction by cytochrome p450.

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

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.

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.

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

Samuel Genheden, Paulius Mikulskis, Ulf Ryde, 2012 .

Will molecular dynamics simulations of proteins ever reach equilibrium?

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

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

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

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.

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

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

EXAFS structure refinement supplemented by computational chemistry

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

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.

Protein Influence on Electronic Spectra Modeled by Multipoles and Polarizabilities.

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

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.

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 .

General Transition-State Force Field for Cytochrome P450 Hydroxylation.

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

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.

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.

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.

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.

Quantum mechanical free energy barrier for an enzymatic reaction.

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

Transferability of conformational dependent charges from protein simulations

Samuel Genheden, Pär Söderhjelm, Ulf Ryde, 2012 .

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 .

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.

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.

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

Ulf Ryde, Emma Sigfridsson, 1998 .

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.

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

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