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Ulf Ryde, Ph.D. - Publications

Affiliations: 
Chemistry Lund University, Lund, Skåne län, Sweden 
Area:
Theoretical Chemistry
Website:
http://www.teokem.lu.se/~ulf/

250 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
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  0.377
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  0.477
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  0.387
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  0.416
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  0.47
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  0.423
2018 Hedegård ED, Ryde U. Molecular mechanism of lytic polysaccharide monooxygenases. Chemical Science. 9: 3866-3880. PMID 29780519 DOI: 10.1039/C8Sc00426A  0.441
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  0.405
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  0.381
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  0.332
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  0.396
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  0.774
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  0.439
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  0.479
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  0.77
2016 Ryde U, Söderhjelm P. Ligand-Binding Affinity Estimates Supported by Quantum-Mechanical Methods. Chemical Reviews. PMID 27077817 DOI: 10.1021/Acs.Chemrev.5B00630  0.775
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  0.437
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  0.768
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  0.726
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  0.529
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  0.581
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  0.499
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  0.753
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  0.773
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  0.615
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  0.744
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  0.786
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  0.572
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  0.764
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  0.372
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  0.328
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  0.681
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  0.358
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  0.439
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  0.309
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  0.729
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  0.786
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  0.735
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  0.723
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  0.805
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  0.71
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  0.737
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  0.482
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  0.805
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  0.439
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  0.767
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  0.757
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  0.776
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  0.673
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  0.759
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  0.762
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  0.382
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  0.724
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  0.793
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  0.763
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  0.736
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  0.379
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  0.786
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  0.605
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  0.768
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  0.698
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  0.436
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  0.557
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  0.315
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  0.777
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  0.651
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  0.448
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  0.676
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  0.745
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  0.412
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  0.314
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  0.728
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  0.642
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  0.67
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  0.461
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  0.74
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  0.391
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  0.649
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  0.473
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  0.562
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  0.378
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  0.396
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  0.355
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  0.437
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  0.36
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  0.382
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  0.376
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  0.456
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  0.406
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  0.62
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  0.608
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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