| Year |
Citation |
Score |
| 2024 |
Vysotskiy VP, Filippi C, Ryde U. Scalar Relativistic All-Electron and Pseudopotential Study of a Minimal Nitrogenase [Fe(SH)H] Model Employing Coupled-Cluster and Auxiliary-Field Quantum Monte Carlo Many-Body Methods. The Journal of Physical Chemistry. A. 128: 1358-1374. PMID 38324717 DOI: 10.1021/acs.jpca.3c05808 |
0.365 |
|
| 2023 |
Zhai H, Lee S, Cui ZH, Cao L, Ryde U, Chan GK. Multireference Protonation Energetics of a Dimeric Model of Nitrogenase Iron-Sulfur Clusters. The Journal of Physical Chemistry. A. PMID 37967028 DOI: 10.1021/acs.jpca.3c06142 |
0.307 |
|
| 2023 |
Vysotskiy VP, Torbjörnsson M, Jiang H, Larsson ED, Cao L, Ryde U, Zhai H, Lee S, Chan GK. Assessment of DFT functionals for a minimal nitrogenase [Fe(SH)4H]- model employing state-of-the-art ab initio methods. The Journal of Chemical Physics. 159. PMID 37486046 DOI: 10.1063/5.0152611 |
0.334 |
|
| 2023 |
Shirazi J, Jafari S, Ryde U, Irani M. Catalytic Reaction Mechanism of Glyoxalase II: A Quantum Mechanics/Molecular Mechanics Study. The Journal of Physical Chemistry. B. 127: 4480-4495. PMID 37191640 DOI: 10.1021/acs.jpcb.3c01495 |
0.314 |
|
| 2022 |
Jiang H, Svensson OKG, Ryde U. QM/MM Study of Partial Dissociation of S2B for the E Intermediate of Nitrogenase. Inorganic Chemistry. 61: 18067-18076. PMID 36306385 DOI: 10.1021/acs.inorgchem.2c02488 |
0.308 |
|
| 2022 |
Ekberg V, Samways ML, Misini Ignjatović M, Essex JW, Ryde U. Comparison of Grand Canonical and Conventional Molecular Dynamics Simulation Methods for Protein-Bound Water Networks. Acs Physical Chemistry Au. 2: 247-259. PMID 35637786 DOI: 10.1021/acsphyschemau.1c00052 |
0.315 |
|
| 2022 |
Jafari S, Tavares Santos YA, Bergmann J, Irani M, Ryde U. Benchmark Study of Redox Potential Calculations for Iron-Sulfur Clusters in Proteins. Inorganic Chemistry. 61: 5991-6007. PMID 35403427 DOI: 10.1021/acs.inorgchem.1c03422 |
0.391 |
|
| 2021 |
Ekberg V, Ryde U. On the Use of Interaction Entropy and Related Methods to Estimate Binding Entropies. Journal of Chemical Theory and Computation. PMID 34254810 DOI: 10.1021/acs.jctc.1c00374 |
0.308 |
|
| 2021 |
Ekberg V, Ryde U. On the Use of Interaction Entropy and Related Methods to Estimate Binding Entropies. Journal of Chemical Theory and Computation. PMID 34254810 DOI: 10.1021/acs.jctc.1c00374 |
0.308 |
|
| 2021 |
Bergmann J, Oksanen E, Ryde U. Quantum-refinement studies of the bidentate ligand of V‑nitrogenase and the protonation state of CO-inhibited Mo‑nitrogenase. Journal of Inorganic Biochemistry. 219: 111426. PMID 33756394 DOI: 10.1016/j.jinorgbio.2021.111426 |
0.319 |
|
| 2021 |
Jafari S, Ryde U, Irani M. 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. PMID 33543623 DOI: 10.1021/acs.jctc.0c01121 |
0.301 |
|
| 2020 |
Cao L, Caldararu O, Ryde U. Does the crystal structure of vanadium nitrogenase contain a reaction intermediate? Evidence from quantum refinement. Journal of Biological Inorganic Chemistry : Jbic : a Publication of the Society of Biological Inorganic Chemistry. PMID 32856107 DOI: 10.1007/S00775-020-01813-Z |
0.414 |
|
| 2020 |
Cao L, Ryde U. NH binding to the nitrogenase FeMo cluster studied by QM/MM methods. Journal of Biological Inorganic Chemistry : Jbic : a Publication of the Society of Biological Inorganic Chemistry. PMID 32266560 DOI: 10.1007/S00775-020-01780-5 |
0.385 |
|
| 2020 |
Bergmann J, Davidson M, Oksanen E, Ryde U, Jayatilaka D. fragHAR: towards quantum-crystallographic X-ray structure refinement for polypeptides and proteins. Iucrj. 7: 158-165. PMID 32148844 DOI: 10.1107/S2052252519015975 |
0.387 |
|
| 2020 |
Jafari S, Ryde U, Fouda AEA, Alavi FS, Dong G, Irani M. Quantum Mechanics/Molecular Mechanics Study of the Reaction Mechanism of Glyoxalase I. Inorganic Chemistry. PMID 32011880 DOI: 10.1021/Acs.Inorgchem.9B03621 |
0.379 |
|
| 2020 |
Cao L, Ryde U. What is the structure of the E4 intermediate in nitrogenase? Journal of Chemical Theory and Computation. PMID 32003999 DOI: 10.1021/Acs.Jctc.9B01254 |
0.355 |
|
| 2020 |
Larsson ED, Dong G, Veryazov V, Ryde U, Hedegård ED. Is density functional theory accurate for lytic polysaccharide monooxygenase enzymes? Dalton Transactions (Cambridge, England : 2003). PMID 31922155 DOI: 10.1039/C9Dt04486H |
0.346 |
|
| 2020 |
Caldararu O, Misini Ignjatović M, Oksanen E, Ryde U. Water structure in solution and crystal molecular dynamics simulations compared to protein crystal structures Rsc Advances. 10: 8435-8443. DOI: 10.1039/C9Ra09601A |
0.304 |
|
| 2020 |
Cao L, Ryde U. Putative reaction mechanism of nitrogenase after dissociation of a sulfide ligand Journal of Catalysis. 391: 247-259. DOI: 10.1016/J.Jcat.2020.08.028 |
0.47 |
|
| 2019 |
Brânzanic AMV, Ryde U, Silaghi-Dumitrescu R. Importance of the iron-sulfur component and of the siroheme modification in the resting state of sulfite reductase. Journal of Inorganic Biochemistry. 203: 110928. PMID 31756559 DOI: 10.1016/J.Jinorgbio.2019.110928 |
0.376 |
|
| 2019 |
Brânzanic AMV, Ryde U, Silaghi-Dumitrescu R. Why does sulfite reductase employ siroheme? Chemical Communications (Cambridge, England). 55: 14047-14049. PMID 31690895 DOI: 10.1039/C9Cc05271B |
0.354 |
|
| 2019 |
Caldararu O, Kumar R, Oksanen E, Logan DT, Ryde U. Are crystallographic B-factors suitable for calculating protein conformational entropy? Physical Chemistry Chemical Physics : Pccp. PMID 31389436 DOI: 10.1039/C9Cp02504A |
0.403 |
|
| 2019 |
Cao L, Börner MC, Bergmann J, Caldararu O, Ryde U. Geometry and Electronic Structure of the P-Cluster in Nitrogenase Studied by Combined Quantum Mechanical and Molecular Mechanical Calculations and Quantum Refinement. Inorganic Chemistry. PMID 31282663 DOI: 10.1021/Acs.Inorgchem.9B00400 |
0.38 |
|
| 2019 |
Kumar R, Ignjatović MM, Peterson K, Olsson M, Leffler H, Ryde U, Nilsson UJ, Logan DT. Structure and energetics of ligand-fluorine interactions with galectin-3 backbone and side-chain amides - insight into solvation effects and multipolar interactions. Chemmedchem. PMID 31246331 DOI: 10.2210/Pdb6Qlo/Pdb |
0.378 |
|
| 2019 |
Caldararu O, Manzoni F, Oksanen E, Logan DT, Ryde U. Refinement of protein structures using a combination of quantum-mechanical calculations with neutron and X-ray crystallographic data. Acta Crystallographica. Section D, Structural Biology. 75: 368-380. PMID 30988254 DOI: 10.1107/S205979831900175X |
0.315 |
|
| 2019 |
Wang M, Mei Y, Ryde U. Host-guest relative binding affinities at density-functional theory level from semiempirical molecular dynamics simulations. Journal of Chemical Theory and Computation. PMID 30811192 DOI: 10.1021/Acs.Jctc.8B01280 |
0.476 |
|
| 2019 |
Caldararu O, Oksanen E, Ryde U, Hedegård ED. Mechanism of hydrogen peroxide formation by lytic polysaccharide monooxygenase. Chemical Science. 10: 576-586. PMID 30746099 DOI: 10.1039/C8Sc03980A |
0.44 |
|
| 2019 |
Cao L, Ryde U. Extremely large differences in DFT energies for nitrogenase models. Physical Chemistry Chemical Physics : Pccp. PMID 30652711 DOI: 10.1039/C8Cp06930A |
0.46 |
|
| 2019 |
Kumar R, Peterson K, Misini Ignjatović M, Leffler H, Ryde U, Nilsson UJ, Logan DT. Substituted polyfluoroaryl interactions with an arginine side chain in galectin-3 are governed by steric-, desolvation and electronic conjugation effects. Organic & Biomolecular Chemistry. PMID 30632578 DOI: 10.2210/Pdb6I76/Pdb |
0.389 |
|
| 2019 |
Verteramo ML, Stenström O, Misini Ignjatovic M, Caldararu O, Olsson MA, Manzoni F, Leffler H, Oksanen E, Logan DT, Nilsson UJ, Ryde U, Akke M. Interplay between Conformational Entropy and Solvation Entropy in Protein-Ligand Binding. Journal of the American Chemical Society. PMID 30618244 DOI: 10.1021/Jacs.8B11099 |
0.424 |
|
| 2019 |
Caldararu O, Ignjatovic MM, Oksanen E, Ryde U. Improving identification and validation of water molecules in protein crystal structures with molecular dynamics simulations Acta Crystallographica Section A. 75. DOI: 10.1107/S2053273319093896 |
0.308 |
|
| 2019 |
Rovaletti A, Bruschi M, Moro G, Cosentino U, Ryde U, Greco C. A thiocarbonate sink on the enzymatic energy landscape of aerobic CO oxidation? Answers from DFT and QM/MM models of Mo Cu CO-dehydrogenases Journal of Catalysis. 372: 201-205. DOI: 10.1016/J.Jcat.2019.02.032 |
0.386 |
|
| 2019 |
Alavi FS, Zahedi M, Safari N, Ryde U. QM/MM study of the conversion of biliverdin into verdoheme by heme oxygenase Theoretical Chemistry Accounts. 138. DOI: 10.1007/S00214-019-2461-Y |
0.415 |
|
| 2018 |
Dong G, Phung QM, Pierloot K, Ryde U. Reaction Mechanism of [NiFe] Hydrogenase Studied by Computational Methods. Inorganic Chemistry. PMID 30500163 DOI: 10.1021/Acs.Inorgchem.8B02590 |
0.498 |
|
| 2018 |
Wang M, Mei Y, Ryde U. Predicting relative binding affinity using non-equilibrium QM/MM simulations. Journal of Chemical Theory and Computation. PMID 30362750 DOI: 10.1021/Acs.Jctc.8B00685 |
0.484 |
|
| 2018 |
Cao L, Caldararu O, Ryde U. Protonation and reduction of the FeMo cluster in nitrogenase studied by QM/MM calculations. Journal of Chemical Theory and Computation. PMID 30354152 DOI: 10.1021/Acs.Jctc.8B00778 |
0.415 |
|
| 2018 |
Caldararu O, Olsson MA, Misini Ignjatović M, Wang M, Ryde U. Binding free energies in the SAMPL6 octa-acid host-guest challenge calculated with MM and QM methods. Journal of Computer-Aided Molecular Design. PMID 30203229 DOI: 10.1007/S10822-018-0158-2 |
0.469 |
|
| 2018 |
Dong G, Ryde U. Reaction mechanism of formate dehydrogenase studied by computational methods. Journal of Biological Inorganic Chemistry : Jbic : a Publication of the Society of Biological Inorganic Chemistry. PMID 30173398 DOI: 10.1007/S00775-018-1608-Y |
0.445 |
|
| 2018 |
Alavi FS, Gheidi M, Zahedi M, Safari N, Ryde U. A novel mechanism of heme degradation to biliverdin studied by QM/MM and QM calculations. Dalton Transactions (Cambridge, England : 2003). PMID 29892759 DOI: 10.1039/C8Dt00064F |
0.422 |
|
| 2018 |
Hedegård ED, Ryde U. Molecular mechanism of lytic polysaccharide monooxygenases. Chemical Science. 9: 3866-3880. PMID 29780519 DOI: 10.1039/C8Sc00426A |
0.44 |
|
| 2018 |
Steinmann C, Olsson MA, Ryde U. Relative Ligand-Binding Free Energies Calculated from Multiple Short QM/MM MD Simulations. Journal of Chemical Theory and Computation. PMID 29768915 DOI: 10.1021/Acs.Jctc.8B00081 |
0.437 |
|
| 2018 |
Cao L, Ryde U. On the Difference Between Additive and Subtractive QM/MM Calculations. Frontiers in Chemistry. 6: 89. PMID 29666794 DOI: 10.3389/Fchem.2018.00089 |
0.404 |
|
| 2018 |
Jafari S, Kazemi N, Ryde U, Irani M. Higher Flexibility of Glu-172 Explains the Unusual Stereospecificity of Glyoxalase I. Inorganic Chemistry. PMID 29634252 DOI: 10.1021/Acs.Inorgchem.7B03215 |
0.38 |
|
| 2018 |
Caldararu O, Feldt M, Cioloboc D, van Severen MC, Starke K, Mata RA, Nordlander E, Ryde U. QM/MM study of the reaction mechanism of sulfite oxidase. Scientific Reports. 8: 4684. PMID 29549261 DOI: 10.1038/S41598-018-22751-6 |
0.795 |
|
| 2018 |
Manzoni F, Ryde U. Assessing the stability of free-energy perturbation calculations by performing variations in the method. Journal of Computer-Aided Molecular Design. PMID 29536221 DOI: 10.1007/S10822-018-0110-5 |
0.462 |
|
| 2018 |
Genoni A, Bucinsky L, Claiser N, Contreras-Garcia J, Dittrich B, Dominiak PM, Espinosa E, Gatti C, Giannozzi P, Gillet JM, Jayatilaka D, Macchi P, Madsen AØ, Massa LJ, Matta CF, ... ... Ryde U, et al. Quantum Crystallography: Current Developments and Future Perspectives. Chemistry (Weinheim An Der Bergstrasse, Germany). PMID 29488652 DOI: 10.1002/Chem.201705952 |
0.319 |
|
| 2018 |
Dong G, Ryde U, Aa Jensen HJ, Hedegård ED. Exploration of H2 binding to the [NiFe]-hydrogenase active site with multiconfigurational density functional theory. Physical Chemistry Chemical Physics : Pccp. 20: 794-801. PMID 29205241 DOI: 10.1039/C7Cp06767D |
0.375 |
|
| 2018 |
Cao L, Ryde U. Influence of the protein and DFT method on the broken-symmetry and spin states in nitrogenase International Journal of Quantum Chemistry. 118: e25627. DOI: 10.1002/Qua.25627 |
0.376 |
|
| 2017 |
Hedegård ED, Ryde U. Multiscale Modelling of Lytic Polysaccharide Monooxygenases. Acs Omega. 2: 536-545. PMID 31457454 DOI: 10.1021/acsomega.6b00521 |
0.331 |
|
| 2017 |
Dong G, Cao L, Ryde U. Insight into the reaction mechanism of lipoyl synthase: a QM/MM study. Journal of Biological Inorganic Chemistry : Jbic : a Publication of the Society of Biological Inorganic Chemistry. PMID 29204715 DOI: 10.1007/S00775-017-1522-8 |
0.395 |
|
| 2017 |
Misini Ignjatović M, Mikulskis P, Söderhjelm P, Ryde U. Can MM/GBSA calculations be sped up by system truncation? Journal of Computational Chemistry. PMID 29178493 DOI: 10.1002/Jcc.25120 |
0.773 |
|
| 2017 |
Cao L, Caldararu O, Rosenzweig AC, Ryde U. Quantum refinement does not support dinuclear copper sites in crystal structures of particulate methane monooxygenase. Angewandte Chemie (International Ed. in English). PMID 29164769 DOI: 10.1002/Anie.201708977 |
0.377 |
|
| 2017 |
Alavi FS, Zahedi M, Safari N, Ryde U. QM/MM Study of the Conversion of Oxophlorin Into Verdoheme by Heme Oxygenase. The Journal of Physical Chemistry. B. PMID 29090581 DOI: 10.1021/Acs.Jpcb.7B08332 |
0.452 |
|
| 2017 |
Manzoni F, Uranga J, Genheden S, Ryde U. Can System Truncation Speed up Ligand-Binding Calculations with Periodic Free-Energy Simulations? Journal of Chemical Information and Modeling. PMID 29076739 DOI: 10.1021/Acs.Jcim.7B00324 |
0.464 |
|
| 2017 |
Ryde U. How many conformations need to be sampled to obtain converged QM/MM energies? The curse of exponential averaging. Journal of Chemical Theory and Computation. PMID 29024586 DOI: 10.1021/Acs.Jctc.7B00826 |
0.438 |
|
| 2017 |
Olsson MA, García-Sosa AT, Ryde U. 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. PMID 28879536 DOI: 10.1007/S10822-017-0056-Z |
0.43 |
|
| 2017 |
Cao L, Caldararu O, Ryde U. Protonation States of Homocitrate and Nearby Residues in Nitrogenase Studied by Computational Methods and Quantum Refinement. The Journal of Physical Chemistry. B. PMID 28783353 DOI: 10.1021/Acs.Jpcb.7B02714 |
0.442 |
|
| 2017 |
Hedegård ED, Ryde U. Targeting the reactive intermediate in polysaccharide monooxygenases. Journal of Biological Inorganic Chemistry : Jbic : a Publication of the Society of Biological Inorganic Chemistry. PMID 28698982 DOI: 10.1007/S00775-017-1480-1 |
0.399 |
|
| 2017 |
Dong G, Phung QM, Hallaert SD, Pierloot K, Ryde U. H2 binding to the active site of [NiFe] hydrogenase studied by multiconfigurational and coupled-cluster methods. Physical Chemistry Chemical Physics : Pccp. PMID 28397891 DOI: 10.1039/C7Cp01331K |
0.507 |
|
| 2017 |
Dong G, Ryde U. Effect of the protein ligand in DMSO reductase studied by computational methods. Journal of Inorganic Biochemistry. 171: 45-51. PMID 28364618 DOI: 10.1016/J.Jinorgbio.2017.03.004 |
0.478 |
|
| 2017 |
Olsson MA, Ryde U. Comparison of methods to obtain ligand-binding free energies with QM/MM methods. Journal of Chemical Theory and Computation. PMID 28355487 DOI: 10.1021/Acs.Jctc.6B01217 |
0.477 |
|
| 2016 |
Dong G, Ryde U. O2 Activation in Salicylate 1,2-Dioxygenase: A QM/MM Study Reveals the Role of His162. Inorganic Chemistry. PMID 27801577 DOI: 10.1021/Acs.Inorgchem.6B01732 |
0.378 |
|
| 2016 |
Fouda A, Ryde U. Does the DFT self-interaction error affect energies calculated in proteins with large QM systems? Journal of Chemical Theory and Computation. PMID 27749065 DOI: 10.1021/Acs.Jctc.6B00903 |
0.478 |
|
| 2016 |
Caldararu O, Olsson MA, Riplinger C, Neese F, Ryde U. Binding free energies in the SAMPL5 octa-acid host-guest challenge calculated with DFT-D3 and CCSD(T). Journal of Computer-Aided Molecular Design. PMID 27600554 DOI: 10.1007/S10822-016-9957-5 |
0.493 |
|
| 2016 |
Misini Ignjatović M, Caldararu O, Dong G, Muñoz-Gutierrez C, Adasme-Carreño F, Ryde U. 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. PMID 27565797 DOI: 10.1007/S10822-016-9942-Z |
0.5 |
|
| 2016 |
Ryde U. QM/MM Calculations on Proteins. Methods in Enzymology. 577: 119-58. PMID 27498637 DOI: 10.1016/Bs.Mie.2016.05.014 |
0.473 |
|
| 2016 |
Olsson MA, Söderhjelm P, Ryde U. Converging ligand-binding free energies obtained with free-energy perturbations at the quantum mechanical level. Journal of Computational Chemistry. PMID 27117350 DOI: 10.1002/Jcc.24375 |
0.769 |
|
| 2016 |
Ryde U, Söderhjelm P. Ligand-Binding Affinity Estimates Supported by Quantum-Mechanical Methods. Chemical Reviews. PMID 27077817 DOI: 10.1021/Acs.Chemrev.5B00630 |
0.774 |
|
| 2016 |
Dong G, Ryde U. Protonation states of intermediates in the reaction mechanism of [NiFe] hydrogenase studied by computational methods. Journal of Biological Inorganic Chemistry : Jbic : a Publication of the Society of Biological Inorganic Chemistry. PMID 26940957 DOI: 10.1007/S00775-016-1348-9 |
0.461 |
|
| 2016 |
Jafari S, Ryde U, Irani M. Catalytic mechanism of human glyoxalase i studied by quantum-mechanical cluster calculations Journal of Molecular Catalysis B: Enzymatic. 131: 18-30. DOI: 10.1016/J.Molcatb.2016.05.010 |
0.436 |
|
| 2015 |
Genheden S, Ryde U, Söderhjelm P. Binding affinities by alchemical perturbation using QM/MM with a large QM system and polarizable MM model. Journal of Computational Chemistry. 36: 2114-24. PMID 26280564 DOI: 10.1002/Jcc.24048 |
0.766 |
|
| 2015 |
Li J, Farrokhnia M, Rulíšek L, Ryde U. Catalytic Cycle of Multicopper Oxidases Studied by Combined Quantum- and Molecular-Mechanical Free-Energy Perturbation Methods. The Journal of Physical Chemistry. B. PMID 26039490 DOI: 10.1021/Acs.Jpcb.5B02864 |
0.721 |
|
| 2015 |
Hedegård ED, Kongsted J, Ryde U. Multiscale modeling of the active site of [fe] hydrogenase: the h2 binding site in open and closed protein conformations. Angewandte Chemie (International Ed. in English). 54: 6246-50. PMID 25867218 DOI: 10.1002/Anie.201501737 |
0.39 |
|
| 2015 |
Genheden S, Ryde U. The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities. Expert Opinion On Drug Discovery. 10: 449-61. PMID 25835573 DOI: 10.1517/17460441.2015.1032936 |
0.437 |
|
| 2015 |
Li X, Siegbahn PE, Ryde U. Simulation of the isotropic EXAFS spectra for the S2 and S3 structures of the oxygen evolving complex in photosystem II. Proceedings of the National Academy of Sciences of the United States of America. 112: 3979-84. PMID 25775575 DOI: 10.1073/Pnas.1422058112 |
0.528 |
|
| 2015 |
Li J, Andreji? M, Mata RA, Ryde U. A Computational Comparison of Oxygen Atom Transfer Catalyzed by Dimethyl Sulf-oxide Reductase with Mo and W European Journal of Inorganic Chemistry. DOI: 10.1002/Ejic.201500209 |
0.58 |
|
| 2014 |
Genheden S, Akke M, Ryde U. Conformational Entropies and Order Parameters: Convergence, Reproducibility, and Transferability. Journal of Chemical Theory and Computation. 10: 432-8. PMID 26579922 DOI: 10.1021/Ct400747S |
0.413 |
|
| 2014 |
Li J, Ryde U. Comparison of the active-site design of molybdenum oxo-transfer enzymes by quantum mechanical calculations. Inorganic Chemistry. 53: 11913-24. PMID 25372012 DOI: 10.1021/Ic5010837 |
0.498 |
|
| 2014 |
Mikulskis P, Genheden S, Ryde U. A large-scale test of free-energy simulation estimates of protein-ligand binding affinities. Journal of Chemical Information and Modeling. 54: 2794-806. PMID 25264937 DOI: 10.1021/Ci5004027 |
0.436 |
|
| 2014 |
Andreji? M, Ryde U, Mata RA, Söderhjelm P. Coupled-cluster interaction energies for 200-atom host-guest systems. Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry. 15: 3270-81. PMID 25262989 DOI: 10.1002/Cphc.201402379 |
0.751 |
|
| 2014 |
van Severen MC, Andreji? M, Li J, Starke K, Mata RA, Nordlander E, Ryde U. A quantum-mechanical study of the reaction mechanism of sulfite oxidase. Journal of Biological Inorganic Chemistry : Jbic : a Publication of the Society of Biological Inorganic Chemistry. 19: 1165-79. PMID 24957901 DOI: 10.1007/S00775-014-1172-Z |
0.813 |
|
| 2014 |
Mikulskis P, Genheden S, Ryde U. Effect of explicit water molecules on ligand-binding affinities calculated with the MM/GBSA approach. Journal of Molecular Modeling. 20: 2273. PMID 24869780 DOI: 10.1007/S00894-014-2273-X |
0.386 |
|
| 2014 |
Mikulskis P, Cioloboc D, Andreji? M, Khare S, Brorsson J, Genheden S, Mata RA, Söderhjelm P, Ryde U. Free-energy perturbation and quantum mechanical study of SAMPL4 octa-acid host-guest binding energies. Journal of Computer-Aided Molecular Design. 28: 375-400. PMID 24700414 DOI: 10.1007/S10822-014-9739-X |
0.771 |
|
| 2014 |
Delcey MG, Pierloot K, Phung QM, Vancoillie S, Lindh R, Ryde U. Accurate calculations of geometries and singlet-triplet energy differences for active-site models of [NiFe] hydrogenase. Physical Chemistry Chemical Physics : Pccp. 16: 7927-38. PMID 24647807 DOI: 10.1039/C4Cp00253A |
0.652 |
|
| 2014 |
Sun X, Geng C, Huo R, Ryde U, Bu Y, Li J. Large equatorial ligand effects on C-H bond activation by nonheme iron(IV)-oxo complexes. The Journal of Physical Chemistry. B. 118: 1493-500. PMID 24471414 DOI: 10.1021/Jp410727R |
0.613 |
|
| 2014 |
Hedegård ED, Knecht S, Ryde U, Kongsted J, Saue T. Theoretical 57Fe Mössbauer spectroscopy: isomer shifts of [Fe]-hydrogenase intermediates. Physical Chemistry Chemical Physics : Pccp. 16: 4853-63. PMID 24468665 DOI: 10.1039/C3Cp54393E |
0.409 |
|
| 2014 |
Oksanen E, Blakeley MP, El-Hajji M, Ryde U, Budayova-Spano M. The neutron structure of urate oxidase resolves a long-standing mechanistic conundrum and reveals unexpected changes in protonation. Plos One. 9: e86651. PMID 24466188 DOI: 10.1371/Journal.Pone.0086651 |
0.347 |
|
| 2014 |
Ryde U. A fundamental view of enthalpy-entropy compensation Medchemcomm. 5: 1324-1336. DOI: 10.1039/C4Md00057A |
0.414 |
|
| 2013 |
Sumner S, Söderhjelm P, Ryde U. Effect of Geometry Optimizations on QM-Cluster and QM/MM Studies of Reaction Energies in Proteins. Journal of Chemical Theory and Computation. 9: 4205-14. PMID 26592409 DOI: 10.1021/Ct400339C |
0.743 |
|
| 2013 |
Hu L, Söderhjelm P, Ryde U. Accurate Reaction Energies in Proteins Obtained by Combining QM/MM and Large QM Calculations. Journal of Chemical Theory and Computation. 9: 640-9. PMID 26589061 DOI: 10.1021/Ct3005003 |
0.785 |
|
| 2013 |
Li JL, Mata RA, Ryde U. Large Density-Functional and Basis-Set Effects for the DMSO Reductase Catalyzed Oxo-Transfer Reaction. Journal of Chemical Theory and Computation. 9: 1799-807. PMID 26587636 DOI: 10.1021/Ct301094R |
0.571 |
|
| 2013 |
Van Severen MC, Ryde U, Parisel O, Piquemal JP. Understanding the Chemistry of Lead at a Molecular Level: The Pb(II) 6s6p Lone Pair Can Be Bisdirected in Proteins. Journal of Chemical Theory and Computation. 9: 2416-24. PMID 26583732 DOI: 10.1021/Ct300524V |
0.793 |
|
| 2013 |
Godschalk F, Genheden S, Söderhjelm P, Ryde U. Comparison of MM/GBSA calculations based on explicit and implicit solvent simulations. Physical Chemistry Chemical Physics : Pccp. 15: 7731-9. PMID 23595060 DOI: 10.1039/C3Cp00116D |
0.763 |
|
| 2013 |
Husberg C, Ryde U. How are hydrogen bonds modified by metal binding? Journal of Biological Inorganic Chemistry : Jbic : a Publication of the Society of Biological Inorganic Chemistry. 18: 499-522. PMID 23543233 DOI: 10.1007/S00775-013-0996-2 |
0.376 |
|
| 2013 |
Irani M, Törnvall U, Genheden S, Larsen MW, Hatti-Kaul R, Ryde U. Amino acid oxidation of Candida antarctica lipase B studied by molecular dynamics simulations and site-directed mutagenesis. Biochemistry. 52: 1280-9. PMID 23331091 DOI: 10.1021/Bi301298M |
0.309 |
|
| 2013 |
Li JL, Mata RA, Ryde U. Large density-functional and basis-set effects for the DMSO reductase catalyzed oxo-transfer reaction Journal of Chemical Theory and Computation. 9: 1799-1807. DOI: 10.1021/ct301094r |
0.371 |
|
| 2013 |
Van Severen MC, Ryde U, Parisel O, Piquemal JP. Understanding the chemistry of lead at a molecular level: The Pb(II) 6s6p lone pair can be bisdirected in proteins Journal of Chemical Theory and Computation. 9: 2416-2424. DOI: 10.1021/ct300524v |
0.766 |
|
| 2013 |
Hu L, Söderhjelm P, Ryde U. Accurate reaction energies in proteins obtained by combining QM/MM and large QM calculations Journal of Chemical Theory and Computation. 9: 640-649. DOI: 10.1021/ct3005003 |
0.327 |
|
| 2013 |
RulíŠek L, Ryde U. Theoretical studies of the active-site structure, spectroscopic and thermodynamic properties, and reaction mechanism of multicopper oxidases Coordination Chemistry Reviews. 257: 445-458. DOI: 10.1016/J.Ccr.2012.04.019 |
0.673 |
|
| 2013 |
Li X, Sproviero EM, Ryde U, Batista VS, Chen G. Theoretical EXAFS studies of a model of the oxygen-evolving complex of photosystem II obtained with the quantum cluster approach International Journal of Quantum Chemistry. 113: 474-478. DOI: 10.1002/Qua.24143 |
0.357 |
|
| 2012 |
Genheden S, Ryde U. Improving the Efficiency of Protein-Ligand Binding Free-Energy Calculations by System Truncation. Journal of Chemical Theory and Computation. 8: 1449-58. PMID 26596755 DOI: 10.1021/Ct200853G |
0.484 |
|
| 2012 |
Genheden S, Kuhn O, Mikulskis P, Hoffmann D, Ryde U. The normal-mode entropy in the MM/GBSA method: effect of system truncation, buffer region, and dielectric constant. Journal of Chemical Information and Modeling. 52: 2079-88. PMID 22817270 DOI: 10.1021/Ci3001919 |
0.449 |
|
| 2012 |
Heimdal J, Ryde U. Convergence of QM/MM free-energy perturbations based on molecular-mechanics or semiempirical simulations. Physical Chemistry Chemical Physics : Pccp. 14: 12592-604. PMID 22797613 DOI: 10.1039/C2Cp41005B |
0.438 |
|
| 2012 |
Genheden S, Ryde U. Will molecular dynamics simulations of proteins ever reach equilibrium? Physical Chemistry Chemical Physics : Pccp. 14: 8662-77. PMID 22614001 DOI: 10.1039/C2Cp23961B |
0.405 |
|
| 2012 |
Mikulskis P, Genheden S, Wichmann K, Ryde U. A semiempirical approach to ligand-binding affinities: dependence on the Hamiltonian and corrections. Journal of Computational Chemistry. 33: 1179-89. PMID 22396176 DOI: 10.1002/Jcc.22949 |
0.443 |
|
| 2012 |
Genheden S, Ryde U. Comparison of end-point continuum-solvation methods for the calculation of protein-ligand binding free energies. Proteins. 80: 1326-42. PMID 22274991 DOI: 10.1002/Prot.24029 |
0.488 |
|
| 2012 |
Mikulskis P, Genheden S, Rydberg P, Sandberg L, Olsen L, Ryde U. Binding affinities in the SAMPL3 trypsin and host-guest blind tests estimated with the MM/PBSA and LIE methods. Journal of Computer-Aided Molecular Design. 26: 527-41. PMID 22198518 DOI: 10.1007/S10822-011-9524-Z |
0.379 |
|
| 2012 |
Saraboji K, HÃ¥kansson M, Genheden S, Diehl C, Qvist J, Weininger U, Nilsson UJ, Leffler H, Ryde U, Akke M, Logan DT. The carbohydrate-binding site in galectin-3 is preorganized to recognize a sugarlike framework of oxygens: ultra-high-resolution structures and water dynamics. Biochemistry. 51: 296-306. PMID 22111949 DOI: 10.1021/Bi201459P |
0.391 |
|
| 2012 |
Genheden S, Ryde U. Improving the efficiency of protein-ligand binding free-energy calculations by system truncation Journal of Chemical Theory and Computation. 8: 1449-1458. DOI: 10.1021/ct200853g |
0.31 |
|
| 2012 |
Uranga J, Mikulskis P, Genheden S, Ryde U. Can the protonation state of histidine residues be determined from molecular dynamics simulations? Computational and Theoretical Chemistry. 1000: 75-84. DOI: 10.1016/J.Comptc.2012.09.025 |
0.362 |
|
| 2012 |
Genheden S, Söderhjelm P, Ryde U. Transferability of conformational dependent charges from protein simulations International Journal of Quantum Chemistry. 112: 1768-1785. DOI: 10.1002/Qua.22967 |
0.727 |
|
| 2012 |
Shleev S, Andoralov V, Falk M, Reimann CT, Ruzgas T, Srnec M, Ryde U, Rulíšek L. On the Possibility of Uphill Intramolecular Electron Transfer in Multicopper Oxidases: Electrochemical and Quantum Chemical Study of Bilirubin Oxidase Electroanalysis. 24: 1524-1540. DOI: 10.1002/Elan.201200188 |
0.78 |
|
| 2011 |
Söderhjelm P, Kongsted J, Ryde U. Conformational Dependence of Isotropic Polarizabilities. Journal of Chemical Theory and Computation. 7: 1404-14. PMID 26610132 DOI: 10.1021/Ct100714E |
0.734 |
|
| 2011 |
Hu L, Ryde U. Comparison of Methods to Obtain Force-Field Parameters for Metal Sites. Journal of Chemical Theory and Computation. 7: 2452-2463. PMID 26606619 DOI: 10.1021/Ct100725A |
0.42 |
|
| 2011 |
Genheden S, Ryde U. Comparison of the Efficiency of the LIE and MM/GBSA Methods to Calculate Ligand-Binding Energies. Journal of Chemical Theory and Computation. 7: 3768-78. PMID 26598269 DOI: 10.1021/Ct200163C |
0.468 |
|
| 2011 |
Hu L, Söderhjelm P, Ryde U. On the Convergence of QM/MM Energies. Journal of Chemical Theory and Computation. 7: 761-77. PMID 26596307 DOI: 10.1021/Ct100530R |
0.722 |
|
| 2011 |
Heimdal J, Kaukonen M, Srnec M, Rulíšek L, Ryde U. Reduction potentials and acidity constants of Mn superoxide dismutase calculated by QM/MM free-energy methods. Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry. 12: 3337-47. PMID 21960467 DOI: 10.1002/Cphc.201100339 |
0.8 |
|
| 2011 |
Hu L, Farrokhnia M, Heimdal J, Shleev S, Rulíšek L, Ryde U. Reorganization energy for internal electron transfer in multicopper oxidases. The Journal of Physical Chemistry. B. 115: 13111-26. PMID 21955325 DOI: 10.1021/Jp205897Z |
0.703 |
|
| 2011 |
Greco C, Bruschi M, Fantucci P, Ryde U, De Gioia L. Mechanistic and physiological implications of the interplay among iron-sulfur clusters in [FeFe]-hydrogenases. A QM/MM perspective. Journal of the American Chemical Society. 133: 18742-9. PMID 21942468 DOI: 10.1021/Ja205542K |
0.315 |
|
| 2011 |
Ryde U, Mata RA, Grimme S. Does DFT-D estimate accurate energies for the binding of ligands to metal complexes? Dalton Transactions (Cambridge, England : 2003). 40: 11176-83. PMID 21853206 DOI: 10.1039/C1Dt10867K |
0.485 |
|
| 2011 |
Genheden S, Mikulskis P, Hu L, Kongsted J, Söderhjelm P, Ryde U. Accurate predictions of nonpolar solvation free energies require explicit consideration of binding-site hydration. Journal of the American Chemical Society. 133: 13081-92. PMID 21728337 DOI: 10.1021/Ja202972M |
0.735 |
|
| 2011 |
Ciancetta A, Genheden S, Ryde U. A QM/MM study of the binding of RAPTA ligands to cathepsin B. Journal of Computer-Aided Molecular Design. 25: 729-42. PMID 21701919 DOI: 10.1007/S10822-011-9448-7 |
0.483 |
|
| 2011 |
Yu L, Greco C, Bruschi M, Ryde U, De Gioia L, Reiher M. Targeting intermediates of [FeFe]-hydrogenase by CO and CN vibrational signatures. Inorganic Chemistry. 50: 3888-900. PMID 21443182 DOI: 10.1021/Ic102039Z |
0.333 |
|
| 2011 |
Genheden S, Nilsson I, Ryde U. Binding affinities of factor Xa inhibitors estimated by thermodynamic integration and MM/GBSA. Journal of Chemical Information and Modeling. 51: 947-58. PMID 21417269 DOI: 10.1021/Ci100458F |
0.432 |
|
| 2011 |
Srnec M, Ryde U, Rulísek L. Reductive cleavage of the O-O bond in multicopper oxidases: a QM/MM and QM study. Faraday Discussions. 148: 41-53; discussion 97. PMID 21322476 DOI: 10.1039/C004476H |
0.8 |
|
| 2011 |
Greco C, Bruschi M, Fantucci P, Ryde U, De Gioia L. Isocyanide in biochemistry? A theoretical investigation of the electronic effects and energetics of cyanide ligand protonation in [FeFe]-hydrogenases. Chemistry (Weinheim An Der Bergstrasse, Germany). 17: 1954-65. PMID 21274947 DOI: 10.1002/Chem.201001493 |
0.436 |
|
| 2011 |
Genheden S, Ryde U. A comparison of different initialization protocols to obtain statistically independent molecular dynamics simulations. Journal of Computational Chemistry. 32: 187-95. PMID 21132839 DOI: 10.1002/Jcc.21546 |
0.438 |
|
| 2011 |
Rocha-Rinza T, Sneskov K, Christiansen O, Ryde U, Kongsted J. Unraveling the similarity of the photoabsorption of deprotonated p-coumaric acid in the gas phase and within the photoactive yellow protein. Physical Chemistry Chemical Physics : Pccp. 13: 1585-9. PMID 21132197 DOI: 10.1039/C0Cp01075H |
0.34 |
|
| 2011 |
Genheden S, Ryde U. Comparison of the efficiency of the LIE and MM/GBSA methods to calculate ligand-binding energies Journal of Chemical Theory and Computation. 7: 3768-3778. DOI: 10.1021/ct200163c |
0.328 |
|
| 2011 |
Greco C, Fantucci P, Ryde U, Gioia LD. Fast generation of broken-symmetry states in a large system including multiple iron-sulfur assemblies: Investigation of QM/MM energies, clusters charges, and spin populations International Journal of Quantum Chemistry. 111: 3949-3960. DOI: 10.1002/Qua.22849 |
0.404 |
|
| 2011 |
Greco C, Silakov A, Bruschi M, Ryde U, De Gioia L, Lubitz W. Magnetic properties of [FeFe]-hydrogenases: A theoretical investigation based on extended QM and QM/MM models of the H-cluster and its surroundings European Journal of Inorganic Chemistry. 1043-1049. DOI: 10.1002/Ejic.201001058 |
0.381 |
|
| 2010 |
Genheden S, Kongsted J, Söderhjelm P, Ryde U. Nonpolar Solvation Free Energies of Protein-Ligand Complexes. Journal of Chemical Theory and Computation. 6: 3558-68. PMID 26617102 DOI: 10.1021/Ct100272S |
0.766 |
|
| 2010 |
Genheden S, Diehl C, Akke M, Ryde U. Starting-Condition Dependence of Order Parameters Derived from Molecular Dynamics Simulations. Journal of Chemical Theory and Computation. 6: 2176-90. PMID 26615944 DOI: 10.1021/Ct900696Z |
0.365 |
|
| 2010 |
Söderhjelm P, Kongsted J, Ryde U. Ligand Affinities Estimated by Quantum Chemical Calculations. Journal of Chemical Theory and Computation. 6: 1726-37. PMID 26615702 DOI: 10.1021/Ct9006986 |
0.755 |
|
| 2010 |
Diehl C, Engström O, Delaine T, Håkansson M, Genheden S, Modig K, Leffler H, Ryde U, Nilsson UJ, Akke M. Protein flexibility and conformational entropy in ligand design targeting the carbohydrate recognition domain of galectin-3. Journal of the American Chemical Society. 132: 14577-89. PMID 20873837 DOI: 10.1021/Ja105852Y |
0.376 |
|
| 2010 |
Söderhjelm P, Kongsted J, Genheden S, Ryde U. Estimates of ligand-binding affinities supported by quantum mechanical methods. Interdisciplinary Sciences, Computational Life Sciences. 2: 21-37. PMID 20640794 DOI: 10.1007/S12539-010-0083-0 |
0.775 |
|
| 2010 |
Genheden S, Luchko T, Gusarov S, Kovalenko A, Ryde U. An MM/3D-RISM approach for ligand binding affinities. The Journal of Physical Chemistry. B. 114: 8505-16. PMID 20524650 DOI: 10.1021/Jp101461S |
0.427 |
|
| 2010 |
Fuchs MG, Dechert S, Demeshko S, Ryde U, Meyer F. A five-coordinate [2Fe-2S] cluster. Inorganic Chemistry. 49: 5853-8. PMID 20518488 DOI: 10.1021/Ic902559N |
0.324 |
|
| 2010 |
Vancoillie S, Chalupský J, Ryde U, Solomon EI, Pierloot K, Neese F, Rulísek L. Multireference ab initio calculations of g tensors for trinuclear copper clusters in multicopper oxidases. The Journal of Physical Chemistry. B. 114: 7692-702. PMID 20469875 DOI: 10.1021/Jp103098R |
0.665 |
|
| 2010 |
Bruschi M, Greco C, Bertini L, Fantucci P, Ryde U, De Gioia L. Functionally relevant interplay between the Fe(4)S(4) cluster and CN(-) ligands in the active site of [FeFe]-hydrogenases. Journal of the American Chemical Society. 132: 4992-3. PMID 20302340 DOI: 10.1021/Ja1008773 |
0.343 |
|
| 2010 |
Ryde U, Greco C, De Gioia L. Quantum refinement of [FeFe] hydrogenase indicates a dithiomethylamine ligand. Journal of the American Chemical Society. 132: 4512-3. PMID 20230002 DOI: 10.1021/Ja909194F |
0.414 |
|
| 2010 |
Fuchs MG, Meyer F, Ryde U. A combined computational and experimental investigation of the [2Fe-2S] cluster in biotin synthase. Journal of Biological Inorganic Chemistry : Jbic : a Publication of the Society of Biological Inorganic Chemistry. 15: 203-12. PMID 19768473 DOI: 10.1007/S00775-009-0585-6 |
0.352 |
|
| 2010 |
Genheden S, Ryde U. How to obtain statistically converged MM/GBSA results. Journal of Computational Chemistry. 31: 837-46. PMID 19598265 DOI: 10.1002/Jcc.21366 |
0.413 |
|
| 2009 |
Söderhjelm P, Husberg C, Strambi A, Olivucci M, Ryde U. Protein Influence on Electronic Spectra Modeled by Multipoles and Polarizabilities. Journal of Chemical Theory and Computation. 5: 649-658. PMID 26610229 DOI: 10.1021/Ct800459T |
0.758 |
|
| 2009 |
Wang Y, Shen Y, Ryde U. QM/MM study of the insertion of metal ion into protoporphyrin IX by ferrochelatase. Journal of Inorganic Biochemistry. 103: 1680-6. PMID 19850353 DOI: 10.1016/J.Jinorgbio.2009.09.013 |
0.424 |
|
| 2009 |
Hu L, Eliasson J, Heimdal J, Ryde U. Do quantum mechanical energies calculated for small models of protein-active sites converge? The Journal of Physical Chemistry. A. 113: 11793-800. PMID 19785474 DOI: 10.1021/Jp9029024 |
0.474 |
|
| 2009 |
Diehl C, Genheden S, Modig K, Ryde U, Akke M. Conformational entropy changes upon lactose binding to the carbohydrate recognition domain of galectin-3. Journal of Biomolecular Nmr. 45: 157-69. PMID 19641853 DOI: 10.1007/S10858-009-9356-5 |
0.387 |
|
| 2009 |
Söderhjelm P, Aquilante F, Ryde U. Calculation of protein-ligand interaction energies by a fragmentation approach combining high-level quantum chemistry with classical many-body effects. The Journal of Physical Chemistry. B. 113: 11085-94. PMID 19618955 DOI: 10.1021/Jp810551H |
0.76 |
|
| 2009 |
Zoppellaro G, Bren KL, Ensign AA, Harbitz E, Kaur R, Hersleth HP, Ryde U, Hederstedt L, Andersson KK. Review: studies of ferric heme proteins with highly anisotropic/highly axial low spin (S = 1/2) electron paramagnetic resonance signals with bis-histidine and histidine-methionine axial iron coordination. Biopolymers. 91: 1064-82. PMID 19536822 DOI: 10.1002/Bip.21267 |
0.329 |
|
| 2009 |
Ryde U, Schulzke C, Starke K. Which functional groups of the molybdopterin ligand should be considered when modeling the active sites of the molybdenum and tungsten cofactors? A density functional theory study. Journal of Biological Inorganic Chemistry : Jbic : a Publication of the Society of Biological Inorganic Chemistry. 14: 1053-64. PMID 19479286 DOI: 10.1007/S00775-009-0548-Y |
0.383 |
|
| 2009 |
Kongsted J, Söderhjelm P, Ryde U. How accurate are continuum solvation models for drug-like molecules? Journal of Computer-Aided Molecular Design. 23: 395-409. PMID 19444622 DOI: 10.1007/S10822-009-9271-6 |
0.722 |
|
| 2009 |
Srnec M, Aquilante F, Ryde U, Rulísek L. Reaction mechanism of manganese superoxide dismutase studied by combined quantum and molecular mechanical calculations and multiconfigurational methods. The Journal of Physical Chemistry. B. 113: 6074-86. PMID 19344143 DOI: 10.1021/Jp810247U |
0.788 |
|
| 2009 |
Söderhjelm P, Ryde U. How accurate can a force field become? A polarizable multipole model combined with fragment-wise quantum-mechanical calculations. The Journal of Physical Chemistry. A. 113: 617-27. PMID 19093829 DOI: 10.1021/Jp8073514 |
0.762 |
|
| 2009 |
Kongsted J, Ryde U. An improved method to predict the entropy term with the MM/PBSA approach. Journal of Computer-Aided Molecular Design. 23: 63-71. PMID 18781280 DOI: 10.1007/S10822-008-9238-Z |
0.425 |
|
| 2009 |
Söderhjelm P, Ryde U. Conformational dependence of charges in protein simulations. Journal of Computational Chemistry. 30: 750-60. PMID 18773405 DOI: 10.1002/Jcc.21097 |
0.734 |
|
| 2009 |
Jensen KP, Ryde U. Cobalamins uncovered by modern electronic structure calculations Coordination Chemistry Reviews. 253: 769-778. DOI: 10.1016/J.Ccr.2008.04.015 |
0.378 |
|
| 2008 |
Rydberg P, Ryde U, Olsen L. Sulfoxide, Sulfur, and Nitrogen Oxidation and Dealkylation by Cytochrome P450. Journal of Chemical Theory and Computation. 4: 1369-77. PMID 26631712 DOI: 10.1021/Ct800101V |
0.313 |
|
| 2008 |
Kaukonen M, Söderhjelm P, Heimdal J, Ryde U. Proton Transfer at Metal Sites in Proteins Studied by Quantum Mechanical Free-Energy Perturbations. Journal of Chemical Theory and Computation. 4: 985-1001. PMID 26621239 DOI: 10.1021/Ct700347H |
0.784 |
|
| 2008 |
Rydberg P, Hansen SM, Kongsted J, Norrby PO, Olsen L, Ryde U. Transition-State Docking of Flunitrazepam and Progesterone in Cytochrome P450. Journal of Chemical Theory and Computation. 4: 673-81. PMID 26620942 DOI: 10.1021/Ct700313J |
0.601 |
|
| 2008 |
Rydberg P, Ryde U, Olsen L. Prediction of activation energies for aromatic oxidation by cytochrome P450. The Journal of Physical Chemistry. A. 112: 13058-65. PMID 18986131 DOI: 10.1021/Jp803854V |
0.458 |
|
| 2008 |
Kaukonen M, Söderhjelm P, Heimdal J, Ryde U. QM/MM-PBSA method to estimate free energies for reactions in proteins. The Journal of Physical Chemistry. B. 112: 12537-48. PMID 18781715 DOI: 10.1021/Jp802648K |
0.767 |
|
| 2008 |
Devarajan A, Gaenko AV, Ryde U. Effect of covalent links on the structure, spectra, and redox properties of myeloperoxidase--a density functional study. Journal of Inorganic Biochemistry. 102: 1549-57. PMID 18331758 DOI: 10.1016/J.Jinorgbio.2008.01.031 |
0.336 |
|
| 2008 |
Ballmann J, Dechert S, Bill E, Ryde U, Meyer F. Secondary bonding interactions in biomimetic [2Fe-2S] clusters. Inorganic Chemistry. 47: 1586-96. PMID 18257548 DOI: 10.1021/Ic702095A |
0.372 |
|
| 2008 |
Heimdal J, Rydberg P, Ryde U. Protonation of the proximal histidine ligand in heme peroxidases. The Journal of Physical Chemistry. B. 112: 2501-10. PMID 18251539 DOI: 10.1021/Jp710038S |
0.492 |
|
| 2008 |
Söderhjelm P, Ohrn A, Ryde U, Karlström G. Accuracy of typical approximations in classical models of intermolecular polarization. The Journal of Chemical Physics. 128: 014102. PMID 18190180 DOI: 10.1063/1.2814240 |
0.696 |
|
| 2008 |
Rydberg P, Hansen SM, Kongsted J, Norrby PO, Olsen L, Ryde U. Transition-state docking of flunitrazepam and progesterone in cytochrome P450 Journal of Chemical Theory and Computation. 4: 673-681. DOI: 10.1021/ct700313j |
0.43 |
|
| 2008 |
Bruschi M, Greco C, Zampella G, Ryde U, Pickett CJ, De Gioia L. A DFT investigation on structural and redox properties of a synthetic Fe6S6 assembly closely related to the [FeFe]-hydrogenases active site Comptes Rendus Chimie. 11: 834-841. DOI: 10.1016/J.Crci.2008.04.010 |
0.337 |
|
| 2007 |
Rydberg P, Olsen L, Norrby PO, Ryde U. General Transition-State Force Field for Cytochrome P450 Hydroxylation. Journal of Chemical Theory and Computation. 3: 1765-73. PMID 26627620 DOI: 10.1021/Ct700110F |
0.553 |
|
| 2007 |
Kongsted J, Ryde U, Wydra J, Jensen JH. Prediction and rationalization of the pH dependence of the activity and stability of family 11 xylanases. Biochemistry. 46: 13581-92. PMID 17960918 DOI: 10.1021/Bi7016365 |
0.316 |
|
| 2007 |
Greco C, Bruschi M, Heimdal J, Fantucci P, De Gioia L, Ryde U. Structural insights into the active-ready form of [FeFe]-hydrogenase and mechanistic details of its inhibition by carbon monoxide. Inorganic Chemistry. 46: 7256-8. PMID 17676838 DOI: 10.1021/Ic701051H |
0.38 |
|
| 2007 |
Greco C, Bruschi M, De Gioia L, Ryde U. A QM/MM investigation of the activation and catalytic mechanism of Fe-only hydrogenases. Inorganic Chemistry. 46: 5911-21. PMID 17602468 DOI: 10.1021/Ic062320A |
0.369 |
|
| 2007 |
Söderhjelm P, Krogh JW, Karlström G, Ryde U, Lindh R. Accuracy of distributed multipoles and polarizabilities: comparison between the LoProp and MpProp models. Journal of Computational Chemistry. 28: 1083-90. PMID 17279548 DOI: 10.1002/Jcc.20632 |
0.776 |
|
| 2007 |
Ryde U. Accurate metal-site structures in proteins obtained by combining experimental data and quantum chemistry. Dalton Transactions (Cambridge, England : 2003). 607-25. PMID 17268593 DOI: 10.1039/B614448A |
0.41 |
|
| 2007 |
Ryde U, Hsiao YW, Rulísek L, Solomon EI. Identification of the peroxy adduct in multicopper oxidases by a combination of computational chemistry and extended X-ray absorption fine-structure measurements. Journal of the American Chemical Society. 129: 726-7. PMID 17243785 DOI: 10.1021/Ja062954G |
0.643 |
|
| 2007 |
Jensen KP, Roos BO, Ryde U. Performance of density functionals for first row transition metal systems. The Journal of Chemical Physics. 126: 014103. PMID 17212486 DOI: 10.1063/1.2406071 |
0.546 |
|
| 2007 |
Heimdal J, Jensen KP, Devarajan A, Ryde U. The role of axial ligands for the structure and function of chlorophylls. Journal of Biological Inorganic Chemistry : Jbic : a Publication of the Society of Biological Inorganic Chemistry. 12: 49-61. PMID 16953415 DOI: 10.1007/S00775-006-0164-Z |
0.436 |
|
| 2007 |
Rydberg P, Olsen L, Norrby PO, Ryde U. General transition-state force field for cytochrome P450 hydroxylation Journal of Chemical Theory and Computation. 3: 1765-1773. DOI: 10.1021/ct700110f |
0.442 |
|
| 2006 |
Chalupský J, Neese F, Solomon EI, Ryde U, Rulísek L. Multireference ab initio calculations on reaction intermediates of the multicopper oxidases. Inorganic Chemistry. 45: 11051-9. PMID 17173465 DOI: 10.1021/Ic0619512 |
0.668 |
|
| 2006 |
Weis A, Katebzadeh K, Söderhjelm P, Nilsson I, Ryde U. Ligand affinities predicted with the MM/PBSA method: dependence on the simulation method and the force field. Journal of Medicinal Chemistry. 49: 6596-606. PMID 17064078 DOI: 10.1021/Jm0608210 |
0.744 |
|
| 2006 |
Olsen L, Rydberg P, Rod TH, Ryde U. Prediction of activation energies for hydrogen abstraction by cytochrome p450. Journal of Medicinal Chemistry. 49: 6489-99. PMID 17064067 DOI: 10.1021/Jm060551L |
0.411 |
|
| 2006 |
Karlberg T, Schagerlöf U, Gakh O, Park S, Ryde U, Lindahl M, Leath K, Garman E, Isaya G, Al-Karadaghi S. The structures of frataxin oligomers reveal the mechanism for the delivery and detoxification of iron. Structure (London, England : 1993). 14: 1535-46. PMID 17027502 DOI: 10.1016/J.Str.2006.08.010 |
0.315 |
|
| 2006 |
Söderhjelm P, Karlström G, Ryde U. Comparison of overlap-based models for approximating the exchange-repulsion energy. The Journal of Chemical Physics. 124: 244101. PMID 16821967 DOI: 10.1063/1.2206182 |
0.726 |
|
| 2006 |
Rulísek L, Jensen KP, Lundgren K, Ryde U. The reaction mechanism of iron and manganese superoxide dismutases studied by theoretical calculations. Journal of Computational Chemistry. 27: 1398-414. PMID 16802319 DOI: 10.1002/Jcc.20450 |
0.634 |
|
| 2006 |
Gaenko AV, Devarajan A, Tselinskii IV, Ryde U. Structural and photoluminescence properties of excited state intramolecular proton transfer capable compounds-potential emissive and electron transport materials. The Journal of Physical Chemistry. A. 110: 7935-42. PMID 16789783 DOI: 10.1021/Jp060646Z |
0.332 |
|
| 2006 |
Rulísek L, Ryde U. Structure of reduced and oxidized manganese superoxide dismutase: a combined computational and experimental approach. The Journal of Physical Chemistry. B. 110: 11511-8. PMID 16771427 DOI: 10.1021/Jp057295T |
0.662 |
|
| 2006 |
Rod TH, Rydberg P, Ryde U. Implicit versus explicit solvent in free energy calculations of enzyme catalysis: Methyl transfer catalyzed by catechol O-methyltransferase. The Journal of Chemical Physics. 124: 174503. PMID 16689579 DOI: 10.1063/1.2186635 |
0.412 |
|
| 2006 |
Hersleth HP, Ryde U, Rydberg P, Görbitz CH, Andersson KK. Structures of the high-valent metal-ion haem-oxygen intermediates in peroxidases, oxygenases and catalases. Journal of Inorganic Biochemistry. 100: 460-76. PMID 16510192 DOI: 10.1016/J.Jinorgbio.2006.01.018 |
0.401 |
|
| 2006 |
Hsiao YW, Tao Y, Shokes JE, Scott RA, Ryde U. EXAFS structure refinement supplemented by computational chemistry Physical Review B - Condensed Matter and Materials Physics. 74. DOI: 10.1103/Physrevb.74.214101 |
0.46 |
|
| 2006 |
Söderhjelm P, Ryde U. Combined computational and crystallographic study of the oxidised states of [NiFe] hydrogenase Journal of Molecular Structure: Theochem. 770: 199-219. DOI: 10.1016/J.Theochem.2006.06.008 |
0.738 |
|
| 2006 |
Hsiao YW, Ryde U. Interpretation of EXAFS spectra for sitting-atop complexes with the help of computational methods Inorganica Chimica Acta. 359: 1081-1092. DOI: 10.1016/J.Ica.2005.11.036 |
0.39 |
|
| 2005 |
Rod TH, Ryde U. Accurate QM/MM Free Energy Calculations of Enzyme Reactions: Methylation by Catechol O-Methyltransferase. Journal of Chemical Theory and Computation. 1: 1240-51. PMID 26631668 DOI: 10.1021/Ct0501102 |
0.488 |
|
| 2005 |
Rulísek L, Solomon EI, Ryde U. A combined quantum and molecular mechanical study of the O2 reductive cleavage in the catalytic cycle of multicopper oxidases. Inorganic Chemistry. 44: 5612-28. PMID 16060610 DOI: 10.1021/Ic050092Z |
0.641 |
|
| 2005 |
Jensen KP, Ryde U. How the Co-C bond is cleaved in coenzyme B12 enzymes: a theoretical study. Journal of the American Chemical Society. 127: 9117-28. PMID 15969590 DOI: 10.1021/Ja050744I |
0.388 |
|
| 2005 |
Rod TH, Ryde U. Quantum mechanical free energy barrier for an enzymatic reaction. Physical Review Letters. 94: 138302. PMID 15904045 DOI: 10.1103/Physrevlett.94.138302 |
0.472 |
|
| 2005 |
Hsiao YW, Drakenberg T, Ryde U. NMR structure determination of proteins supplemented by quantum chemical calculations: detailed structure of the Ca2+ sites in the EGF34 fragment of protein S. Journal of Biomolecular Nmr. 31: 97-114. PMID 15772750 DOI: 10.1007/S10858-004-6729-7 |
0.427 |
|
| 2005 |
Ryabova ES, Rydberg P, Kolberg M, Harbitz E, Barra AL, Ryde U, Andersson KK, Nordlander E. A comparative reactivity study of microperoxidases based on hemin, mesohemin and deuterohemin. Journal of Inorganic Biochemistry. 99: 852-63. PMID 15708807 DOI: 10.1016/J.Jinorgbio.2004.12.020 |
0.318 |
|
| 2005 |
Shen Y, Ryde U. Reaction mechanism of porphyrin metallation studied by theoretical methods. Chemistry (Weinheim An Der Bergstrasse, Germany). 11: 1549-64. PMID 15662683 DOI: 10.1002/Chem.200400298 |
0.389 |
|
| 2005 |
Jensen KP, Roos BO, Ryde U. O2-binding to heme: electronic structure and spectrum of oxyheme, studied by multiconfigurational methods. Journal of Inorganic Biochemistry. 99: 45-54. PMID 15598490 DOI: 10.1016/J.Jinorgbio.2004.11.008 |
0.561 |
|
| 2005 |
Jensen KP, Ryde U. Comparison of chemical properties of iron, cobalt, and nickel porphyrins, corrins, and hydrocorphins Journal of Porphyrins and Phthalocyanines. 9: 581-606. DOI: 10.1142/S1088424605000691 |
0.366 |
|
| 2005 |
Jensen KP, Roos BO, Ryde U. Erratum to “O2-binding to heme: electronic structure and spectrum of oxyheme, studied by multiconfigurational methods” [J. Inorg. Biochem. 99(1) (2004) 45–54] Journal of Inorganic Biochemistry. 99: 978. DOI: 10.1016/J.Jinorgbio.2005.02.013 |
0.518 |
|
| 2005 |
Källrot N, Nilsson K, Rasmussen T, Ryde U. Theoretical study of structure of catalytic copper site in nitrite reductase International Journal of Quantum Chemistry. 102: 520-541. DOI: 10.1002/Qua.20386 |
0.476 |
|
| 2004 |
Nilsson K, Hersleth HP, Rod TH, Andersson KK, Ryde U. The protonation status of compound II in myoglobin, studied by a combination of experimental data and quantum chemical calculations: quantum refinement. Biophysical Journal. 87: 3437-47. PMID 15339813 DOI: 10.1529/Biophysj.104.041590 |
0.437 |
|
| 2004 |
Nilsson K, Ryde U. Protonation status of metal-bound ligands can be determined by quantum refinement. Journal of Inorganic Biochemistry. 98: 1539-46. PMID 15337606 DOI: 10.1016/J.Jinorgbio.2004.06.006 |
0.437 |
|
| 2004 |
Shen Y, Ryde U. The structure of sitting-atop complexes of metalloporphyrins studied by theoretical methods. Journal of Inorganic Biochemistry. 98: 878-95. PMID 15134934 DOI: 10.1016/J.Jinorgbio.2004.01.004 |
0.385 |
|
| 2004 |
Jensen KP, Ryde U. How O2 binds to heme: reasons for rapid binding and spin inversion. The Journal of Biological Chemistry. 279: 14561-9. PMID 14752099 DOI: 10.1074/Jbc.M314007200 |
0.377 |
|
| 2004 |
Rydberg P, Sigfridsson E, Ryde U. On the role of the axial ligand in heme proteins: a theoretical study. Journal of Biological Inorganic Chemistry : Jbic : a Publication of the Society of Biological Inorganic Chemistry. 9: 203-23. PMID 14727167 DOI: 10.1007/S00775-003-0515-Y |
0.395 |
|
| 2004 |
Olsen L, Rasmussen T, Hemmingsen L, Ryde U. Binding of benzylpenicillin to metallo-β-lactamase ase: A QM/MM study Journal of Physical Chemistry B. 108: 17639-17648. DOI: 10.1021/Jp0482215 |
0.358 |
|
| 2004 |
Roos BO, Ryde U. Molecular Orbital Theory (SCF Methods and Active Space SCF) Comprehensive Coordination Chemistry Ii. 2: 519-539. DOI: 10.1016/B0-08-043748-6/01245-7 |
0.45 |
|
| 2003 |
Ryde U, Nilsson K. Quantum chemistry can locally improve protein crystal structures. Journal of the American Chemical Society. 125: 14232-3. PMID 14624544 DOI: 10.1021/Ja0365328 |
0.375 |
|
| 2003 |
Jensen KP, Ryde U. Conversion of homocysteine to methionine by methionine synthase: a density functional study. Journal of the American Chemical Society. 125: 13970-1. PMID 14611228 DOI: 10.1021/Ja034697A |
0.371 |
|
| 2003 |
Lecerof D, Fodje MN, Alvarez León R, Olsson U, Hansson A, Sigfridsson E, Ryde U, Hansson M, Al-Karadaghi S. Metal binding to Bacillus subtilis ferrochelatase and interaction between metal sites. Journal of Biological Inorganic Chemistry : Jbic : a Publication of the Society of Biological Inorganic Chemistry. 8: 452-8. PMID 12761666 DOI: 10.1007/S00775-002-0436-1 |
0.311 |
|
| 2003 |
Jensen KP, Ryde U. Comparison of the chemical properties of iron and cobalt porphyrins and corrins. Chembiochem : a European Journal of Chemical Biology. 4: 413-24. PMID 12740813 DOI: 10.1002/Cbic.200200449 |
0.356 |
|
| 2003 |
Sigfridsson E, Ryde U. The importance of porphyrin distortions for the ferrochelatase reaction Journal of Biological Inorganic Chemistry. 8: 273-282. PMID 12589563 DOI: 10.1007/S00775-002-0413-8 |
0.445 |
|
| 2003 |
Nilsson K, Lecerof D, Sigfridsson E, Ryde U. An automatic method to generate force-field parameters for hetero-compounds Acta Crystallographica - Section D Biological Crystallography. 59: 274-289. PMID 12554938 DOI: 10.1107/S0907444902021431 |
0.374 |
|
| 2003 |
Ryde U. Combined quantum and molecular mechanics calculations on metalloproteins Current Opinion in Chemical Biology. 7: 136-142. PMID 12547438 DOI: 10.1016/S1367-5931(02)00016-9 |
0.436 |
|
| 2003 |
Gerlach LO, Jakobsen JS, Jensen KP, Rosenkilde MR, Skerlj RT, Ryde U, Bridger GJ, Schwartz TW. Metal ion enhanced binding of AMD3100 to Asp262 in the CXCR4 receptor Biochemistry. 42: 710-717. PMID 12534283 DOI: 10.1021/Bi0264770 |
0.324 |
|
| 2003 |
Jensen KP, Ryde U. Importance of proximal hydrogen bonds in haem proteins Molecular Physics. 101: 2003-2018. DOI: 10.1080/0026897031000109383 |
0.362 |
|
| 2003 |
Olsen L, Antony J, Ryde U, Adolph HW, Hemmingsen L. Lactam hydrolysis catalyzed by mononuclear metallo-β-lactamases: A density functional study Journal of Physical Chemistry B. 107: 2366-2375. DOI: 10.1021/Jp0275950 |
0.359 |
|
| 2003 |
Jensen KP, Ryde U. Theoretical Prediction of the Co-C Bond Strength in Cobalamins Journal of Physical Chemistry A. 107: 7539-7545. DOI: 10.1021/Jp027566P |
0.414 |
|
| 2003 |
Karlström G, Lindh R, Malmqvist PA, Roos BO, Ryde U, Veryazov V, Widmark PO, Cossi M, Schimmelpfennig B, Neogrady P, Seijo L. MOLCAS: A program package for computational chemistry Computational Materials Science. 28: 222-239. DOI: 10.1016/S0927-0256(03)00109-5 |
0.696 |
|
| 2003 |
Ryde U, Nilsson K. Quantum refinement - A combination of quantum chemistry and protein crystallography Journal of Molecular Structure: Theochem. 632: 259-275. DOI: 10.1016/S0166-1280(03)00304-X |
0.389 |
|
| 2003 |
Ryde U, Nilsson K. Quantum refinement — a method to determine protonation and oxidation states of metal sites in protein crystal structures Journal of Inorganic Biochemistry. 96: 39. DOI: 10.1016/S0162-0134(03)80470-1 |
0.354 |
|
| 2002 |
Sigfridsson E, Ryde U. Theoretical study of the discrimination between O2 and CO by myoglobin Journal of Inorganic Biochemistry. 91: 101-115. PMID 12121767 DOI: 10.1016/S0162-0134(02)00426-9 |
0.381 |
|
| 2002 |
Ryde U, Olsen L, Nilsson K. Quantum chemical geometry optimizations in proteins using crystallographic raw data Journal of Computational Chemistry. 23: 1058-1070. PMID 12116392 DOI: 10.1002/Jcc.10093 |
0.412 |
|
| 2002 |
Sigfridsson E, Ryde U, Bush BL. Restrained point-charge models for disaccharides. Journal of Computational Chemistry. 23: 351-64. PMID 11908498 DOI: 10.1002/Jcc.10024 |
0.352 |
|
| 2002 |
Jensen KP, Ryde U. The axial N-base has minor influence on Co-C bond cleavage in cobalamins Journal of Molecular Structure: Theochem. 585: 239-255. DOI: 10.1016/S0166-1280(02)00049-0 |
0.326 |
|
| 2001 |
Olsson MHM, Ryde U. Geometry, reduction potential, and reorganization energy of the binuclear Cua site, studied by density functional theory Journal of the American Chemical Society. 123: 7866-7876. PMID 11493060 DOI: 10.1021/Ja010315U |
0.375 |
|
| 2001 |
Sigfridsson E, Olsson MHM, Ryde U. Inner-sphere reorganization energy of iron-sulfur clusters studied with theoretical methods Inorganic Chemistry. 40: 2509-2519. PMID 11350228 DOI: 10.1021/Ic000752U |
0.38 |
|
| 2001 |
Sigfridsson E, Olsson MHM, Ryde U. A comparison of the inner-sphere reorganization energies of cytochromes, iron-sulfur clusters, and blue copper proteins Journal of Physical Chemistry B. 105: 5546-5552. DOI: 10.1021/Jp0037403 |
0.455 |
|
| 2001 |
Ryde U, Olsson MHM, Pierloot K. The structure and function of blue copper proteins Theoretical and Computational Chemistry. 9: 1-55. DOI: 10.1016/S1380-7323(01)80002-9 |
0.498 |
|
| 2001 |
Ryde U, Olsson MHM, Roos BO, Borin AC. A theoretical study of the copper-cysteine bond in blue copper proteins Theoretical Chemistry Accounts. 105: 452-462. DOI: 10.1007/S002140000242 |
0.609 |
|
| 2001 |
Ryde U, Olsson MHM. Structure, strain, and reorganization energy of blue copper models in the protein International Journal of Quantum Chemistry. 81: 335-347. DOI: 10.1002/1097-461X(2001)81:5<335::Aid-Qua1003>3.0.Co;2-Q |
0.442 |
|
| 2000 |
Ryde U, Olsson MH, Roos BO, De Kerpel JO, Pierloot K. On the role of strain in blue copper proteins. Journal of Biological Inorganic Chemistry : Jbic : a Publication of the Society of Biological Inorganic Chemistry. 5: 565-74. PMID 11085647 DOI: 10.1007/S007750000147 |
0.542 |
|
| 1999 |
Olsson MHM, Ryde U. The influence of axial ligands on the reduction potential of blue copper proteins Journal of Biological Inorganic Chemistry. 4: 654-663. PMID 10550695 DOI: 10.1007/S007750050389 |
0.394 |
|
| 1999 |
Ryde U. Carboxylate binding modes in zinc proteins: A theoretical study Biophysical Journal. 77: 2777-2787. PMID 10545376 DOI: 10.1016/S0006-3495(99)77110-9 |
0.427 |
|
| 1999 |
Sigfridsson E, Ryde U. On the significance of hydrogen bonds for the discrimination between CO and O2 by myoglobin Journal of Biological Inorganic Chemistry. 4: 99-110. PMID 10499107 DOI: 10.1007/S007750050293 |
0.405 |
|
| 1999 |
De Kerpel JOA, Ryde U. Protein strain in blue copper proteins studied by free energy perturbations Proteins: Structure, Function and Genetics. 36: 157-174. PMID 10398364 DOI: 10.1002/(Sici)1097-0134(19990801)36:2<157::Aid-Prot3>3.0.Co;2-Y |
0.44 |
|
| 1999 |
Hemmingsen L, Ryde U, Bauer R. Nuclear quadrupole interactions in cadmium complexes: Semiempirical and ab initio calculations Zeitschrift Fur Naturforschung - Section a Journal of Physical Sciences. 54: 422-430. DOI: 10.1515/Zna-1999-6-713 |
0.402 |
|
| 1999 |
De Kerpel JOA, Pierloot K, Ryde U. Geometric and Electronic Structure of Co(II)-Substituted Azurin Journal of Physical Chemistry B. 103: 8375-8382. DOI: 10.1021/Jp991359G |
0.416 |
|
| 1998 |
Olsson MH, Ryde U, Roos BO. Quantum chemical calculations of the reorganization energy of blue-copper proteins. Protein Science : a Publication of the Protein Society. 7: 2659-68. PMID 9865961 DOI: 10.1002/Pro.5560071220 |
0.609 |
|
| 1998 |
De Kerpel JOA, Pierloot K, Ryde U, Roos BO. Theoretical study of the structural and spectroscopic properties of stellacyanin Journal of Physical Chemistry B. 102: 4638-4647. DOI: 10.1021/Jp980455Z |
0.586 |
|
| 1998 |
De Kerpel JOA, Pierloot K, Ryde U, Roos BO. Theoretical Study of the Structural and Spectroscopic Properties of Stellacyanin The Journal of Physical Chemistry B. 102: 4638-4647. DOI: 10.1021/JP980455Z |
0.427 |
|
| 1998 |
Pierloot K, De Kerpel JOA, Ryde U, Olsson MHM, Roos BO. Relation between the structure and spectroscopic properties of blue copper proteins Journal of the American Chemical Society. 120: 13156-13166. DOI: 10.1021/Ja982385F |
0.6 |
|
| 1998 |
Olsson MHM, Ryde U, Roos BO, Pierloot K. On the relative stability of tetragonal and trigonal Cu(II) complexes with relevance to the blue copper proteins Journal of Biological Inorganic Chemistry. 3: 109-125. DOI: 10.1007/S007750050212 |
0.588 |
|
| 1998 |
Sigfridsson E, Ryde U. Comparison of methods for deriving atomic charges from the electrostatic potential and moments Journal of Computational Chemistry. 19: 377-395. DOI: 10.1002/(Sici)1096-987X(199803)19:4<377::Aid-Jcc1>3.0.Co;2-P |
0.386 |
|
| 1997 |
Pierloot K, De Kerpel JOA, Ryde U, Roos BO. Theoretical study of the electronic spectrum of plastocyanin Journal of the American Chemical Society. 119: 218-226. DOI: 10.1021/Ja962381F |
0.583 |
|
| 1997 |
Pierloot K, De Kerpel J, Olsson M, Ryde U, Roos B. The correlation between structure and spectra of blue copper proteins Journal of Inorganic Biochemistry. 67: 43. DOI: 10.1016/S0162-0134(97)89924-2 |
0.496 |
|
| 1997 |
Ryde U, Hemmingsen L. The active-site metal coordination geometry of cadmium-substituted alcohol dehydrogenase: A theoretical interpretation of perturbed angular correlation of γ-ray measurements Journal of Biological Inorganic Chemistry. 2: 567-579. DOI: 10.1007/S007750050171 |
0.404 |
|
| 1997 |
Lindh R, Ryde U, Schütz M. On the significance of the trigger reaction in the action of the calicheamicin γI 1 anti-cancer drug Theoretical Chemistry Accounts. 97: 203-210. DOI: 10.1007/S002140050254 |
0.619 |
|
| 1996 |
Ryde U, Olsson MH, Pierloot K, Roos BO. The cupric geometry of blue copper proteins is not strained. Journal of Molecular Biology. 261: 586-96. PMID 8794878 DOI: 10.1006/Jmbi.1996.0484 |
0.607 |
|
| 1996 |
Hemmingsen L, Ryde U. Ab initio calculations of electric field gradients in cadmium complexes Journal of Physical Chemistry. 100: 4803-4809. DOI: 10.1021/Jp9526410 |
0.391 |
|
| 1996 |
Ryde U. The coordination of the catalytic zinc ion in alcohol dehydrogenase studied by combined quantum-chemical and molecular mechanics calculations Journal of Computer-Aided Molecular Design. 10: 153-164. DOI: 10.1007/Bf00402823 |
0.375 |
|
| 1996 |
Ryde U. The coordination chemistry of the structural zinc ion in alcohol dehydrogenase studied by ab initio quantum chemical calculations European Biophysics Journal. 24: 213-221. DOI: 10.1007/Bf00205102 |
0.419 |
|
| 1995 |
Ryde U. Molecular dynamics simulations of alcohol dehydrogenase with a four- or five-coordinate catalytic zinc ion Proteins: Structure, Function and Genetics. 21: 40-56. PMID 7716168 DOI: 10.1002/Prot.340210106 |
0.37 |
|
| 1995 |
Ryde U. On the role of Glu-68 in alcohol dehydrogenase Protein Science. 4: 1124-1132. PMID 7549877 DOI: 10.1002/Pro.5560040611 |
0.323 |
|
| 1994 |
Ryde U. The coordination chemistry of the catalytic zinc ion in alcohol dehydrogenase studied by ab initio quantum chemical calculations International Journal of Quantum Chemistry. 52: 1229-1243. DOI: 10.1002/Qua.560520508 |
0.42 |
|
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