Ulf Ryde

ProfessorFormer name: Ulf Ryde-Pettersson
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  1. 2019
  2. A thiocarbonate sink on the enzymatic energy landscape of aerobic CO oxidation? Answers from DFT and QM/MM models of Mo–Cu CO-dehydrogenases

    Rovaletti, A., Bruschi, M., Moro, G., Cosentino, U., Ulf Ryde & Greco, C., 2019, In : Journal of Catalysis. p. 201-205 5 p.

    Research output: Contribution to journalArticle

  3. Extremely large differences in DFT energies for nitrogenase models

    Lili Cao & Ulf Ryde, 2019, In : Physical Chemistry Chemical Physics. 21, 5, p. 2480-2488 9 p.

    Research output: Contribution to journalArticle

  4. Mechanism of hydrogen peroxide formation by lytic polysaccharide monooxygenase

    Octav Caldararu, Oksanen, E., Ulf Ryde & Erik D. Hedegård, 2019, In : Chemical Science. 10, 2, p. 576-586 11 p.

    Research output: Contribution to journalArticle

  5. 2018
  6. QM/MM study of the reaction mechanism of sulfite oxidase

    Octav Caldararu, Feldt, M., Cioloboc, D., Van Severen, M. C., Starke, K., Mata, R. A., Ebbe Nordlander & Ulf Ryde, 2018 Dec 1, In : Scientific Reports. 8, 1, 4684.

    Research output: Contribution to journalArticle

  7. Reaction mechanism of formate dehydrogenase studied by computational methods

    Dong, G. & Ulf Ryde, 2018 Dec, In : Journal of Biological Inorganic Chemistry. 23, 8, p. 1243-1254

    Research output: Contribution to journalArticle

  8. Predicting Relative Binding Affinity Using Nonequilibrium QM/MM Simulations

    Wang, M., Mei, Y. & Ulf Ryde, 2018 Oct 26, In : Journal of Chemical Theory and Computation. 14, p. 6613 6622 p.

    Research output: Contribution to journalArticle

  9. Relative Ligand-Binding Free Energies Calculated from Multiple Short QM/MM MD Simulations

    Ulf Ryde, Olsson, M. & Steinmann, C., 2018 May 17, In : Journal of Chemical Theory and Computation. 14, p. 3228 3237 p.

    Research output: Contribution to journalArticle

  10. Higher Flexibility of Glu-172 Explains the Unusual Stereospecificity of Glyoxalase i

    Jafari, S., Kazemi, N., Ulf Ryde & Irani, M., 2018 May 7, In : Inorganic Chemistry. 57, 9, p. 4944-4958 15 p.

    Research output: Contribution to journalArticle

  11. On the difference between additive and subtractive QM/MM calculations

    Lili Cao & Ulf Ryde, 2018 Apr 1, In : Frontiers in Chemistry. 6, APR, 89.

    Research output: Contribution to journalArticle

  12. Molecular mechanism of lytic polysaccharide monooxygenases

    Erik Hedegård & Ulf Ryde, 2018 Mar 26, In : Chemical Science. 9, 15, p. 3866-3880 15 p.

    Research output: Contribution to journalArticle

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

    Majda Misini Ignjatović, Mikulskis, P., Pär Söderhjelm & Ulf Ryde, 2018 Mar 15, In : Journal of Computational Chemistry. 39, 7, p. 361-372 12 p.

    Research output: Contribution to journalArticle

  14. Influence of the protein and DFT method on the broken-symmetry and spin states in nitroge

    Lili Cao & Ulf Ryde, 2018 Mar 14, In : International Journal of Quantum Chemistry. 118, p. 1 16 p., e25627.

    Research output: Contribution to journalArticle

  15. Insight into the reaction mechanism of lipoyl synthase: a QM/MM study

    Dong, G., Lili Cao & Ulf Ryde, 2018 Mar, In : Journal of Biological Inorganic Chemistry. 23, 2, p. 221-229

    Research output: Contribution to journalArticle

  16. Quantum Crystallography: Current Developments and Future Perspectives

    Genoni, A., Bučinský, L., Claiser, N., Contreras‐García, J., Dittrich, B., Ulf Ryde & Grabowsky, S., 2018 Feb 28, In : Chemistry: A European Journal. 24, p. 10881-10905

    Research output: Contribution to journalArticle

  17. A novel mechanism of heme degradation to biliverdin studied by QM/MM and QM calculations

    Alavi, F. S., Gheidi, M., Zahedi, M., Safari, N. & Ulf Ryde, 2018 Jan 1, In : Dalton Transactions. 47, 25, p. 8283-8291 9 p.

    Research output: Contribution to journalArticle

  18. Binding affinities of the farnesoid X receptor in the D3R Grand Challenge 2 estimated by free-energy perturbation and docking

    Olsson, M. A., García-Sosa, A. T. & Ulf Ryde, 2018 Jan, In : Journal of Computer-Aided Molecular Design. 32, 1, p. 211-224

    Research output: Contribution to journalArticle

  19. Exploration of H2 binding to the [NiFe]-hydrogenase active site with multiconfigurational density functional theory

    Dong, G., Ulf Ryde, Aa Jensen, H. J. & Erik D. Hedegård, 2018, In : Physical Chemistry Chemical Physics. 20, 2, p. 794-801 8 p.

    Research output: Contribution to journalArticle

  20. Reaction Mechanism of [NiFe] Hydrogenase Studied by Computational Methods

    Dong, G., Phung, Q. M., Pierloot, K. & Ulf Ryde, 2018, In : Inorganic Chemistry. 57, 24, p. 15289-15298 10 p.

    Research output: Contribution to journalArticle

  21. 2017
  22. QM/MM Study of the Conversion of Oxophlorin into Verdoheme by Heme Oxygenase

    Alavi, F. S., Zahedi, M., Safari, N. & Ulf Ryde, 2017 Dec 28, In : Journal of Physical Chemistry B. 121, 51, p. 11427-11436 10 p.

    Research output: Contribution to journalArticle

  23. Can System Truncation Speed up Ligand-Binding Calculations with Periodic Free-Energy Simulations?

    Manzoni, F., Uranga, J., Genheden, S. & Ulf Ryde, 2017 Nov 27, In : Journal of Chemical Information and Modeling. 57, 11, p. 2865-2873 9 p.

    Research output: Contribution to journalArticle

  24. Effect of the protein ligand in DMSO reductase studied by computational methods

    Dong, G. & Ulf Ryde, 2017 Jun 1, In : Journal of Inorganic Biochemistry. 171, p. 45-51 7 p.

    Research output: Contribution to journalArticle

  25. Comparison of QM/MM Methods To Obtain Ligand-Binding Free Energies

    Olsson, M. A. & Ulf Ryde, 2017 May 9, In : Journal of Chemical Theory and Computation. 13, 5, p. 2245-2253 9 p.

    Research output: Contribution to journalArticle

  26. Binding free energies in the SAMPL5 octa-acid host–guest challenge calculated with DFT-D3 and CCSD(T)

    Octav Caldararu, Olsson, M. A., Riplinger, C., Neese, F. & Ulf Ryde, 2017 Jan, In : Journal of Computer-Aided Molecular Design. 31, 1, p. 87-106

    Research output: Contribution to journalArticle

  27. H2 binding to the active site of [NiFe] hydrogenase studied by multiconfigurational and coupled-cluster methods

    Dong, G., Phung, Q. M., Hallaert, S. D., Pierloot, K. & Ulf Ryde, 2017, In : Physical Chemistry Chemical Physics. 19, 16, p. 10590-10601 12 p.

    Research output: Contribution to journalArticle

  28. Multiscale Modelling of Lytic Polysaccharide Monooxygenases

    Erik Hedegård & Ulf Ryde, 2017, In : ACS Omega. 2, p. 536-545

    Research output: Contribution to journalArticle

  29. 2016
  30. O2 activation in salicylate 1,2-dioxygenase: A QM/MM study reveals the role of His162

    Dong, G. & Ulf Ryde, 2016 Nov 21, In : Inorganic Chemistry. 55, 22, p. 11727-11735 9 p.

    Research output: Contribution to journalArticle

  31. Does the DFT Self-Interaction Error Affect Energies Calculated in Proteins with Large QM Systems?

    Fouda, A. & Ulf Ryde, 2016 Nov 8, In : Journal of Chemical Theory and Computation. 12, 11, p. 5667-5679 13 p.

    Research output: Contribution to journalArticle

  32. Computational Studies of Molybdenum and Tungsten Enzymes

    Ulf Ryde, Dong, G., Li, J., Feldt, M. & Mata, R. A., 2016 Oct 6, Molybdenum and Tungsten Enzymes: Spectroscopic and Theoretical Investigations. Hille, R., Schulzke, C. & Kirk, M. L. (eds.). 7 ed. Royal Society of Chemistry, Vol. 2017-January. p. 275-321 47 p. (RSC Metallobiology; vol. 2017-January, no. 7).

    Research output: Chapter in Book/Report/Conference proceedingBook chapter

  33. Binding-affinity predictions of HSP90 in the D3R Grand Challenge 2015 with docking, MM/GBSA, QM/MM, and free-energy simulations

    Misini Ignjatović, M., Octav Caldararu, Dong, G., Muñoz-Gutierrez, C., Adasme-Carreño, F. & Ulf Ryde, 2016 Sep 1, In : Journal of Computer-Aided Molecular Design. 30, 9, p. 707-730 24 p.

    Research output: Contribution to journalArticle

  34. Catalytic mechanism of human glyoxalase i studied by quantum-mechanical cluster calculations

    Jafari, S., Ulf Ryde & Irani, M., 2016 Sep 1, In : Journal of Molecular Catalysis B: Enzymatic. 131, p. 18-30 13 p.

    Research output: Contribution to journalArticle

  35. Converging ligand-binding free energies obtained with free-energy perturbations at the quantum mechanical level

    Olsson, M. A., Pär Söderhjelm & Ulf Ryde, 2016 Jun 30, In : Journal of Computational Chemistry. 37, 17, p. 1589-1600 12 p.

    Research output: Contribution to journalArticle

  36. Ligand-Binding Affinity Estimates Supported by Quantum-Mechanical Methods

    Ulf Ryde & Pär Söderhjelm, 2016 May 11, In : Chemical Reviews. 116, 9, p. 5520-5566 47 p.

    Research output: Contribution to journalArticle

  37. QM/MM Calculations on Proteins

    U. Ryde, 2016, In : Methods in Enzymology. 577, p. 119–158 40 p.

    Research output: Contribution to journalArticle

  38. 2015
  39. A Computational Comparison of Oxygen Atom Transfer Catalyzed by Dimethyl Sulfoxide Reductase with Mo and W

    Li, J., Andrejic, M., Mata, R. A. & Ulf Ryde, 2015, In : European Journal of Inorganic Chemistry. 21, p. 3580-3589

    Research output: Contribution to journalArticle

  40. Catalytic Cycle of Multicopper Oxidases Studied by Combined Quantum- and Molecular-Mechanical Free-Energy Perturbation Methods.

    Li, J., Farrokhnia, M., Rulisek, L. & Ulf Ryde, 2015, In : The Journal of Physical Chemistry Part B. 119, 26, p. 8268-8284

    Research output: Contribution to journalArticle

  41. Multiscale Modeling of the Active Site of [Fe] Hydrogenase: The H-2 Binding Site in Open and Closed Protein Conformations

    Hedegard, E. D., Kongsted, J. & Ulf Ryde, 2015, In : Angewandte Chemie (International edition). 54, 21, p. 6246-6250

    Research output: Contribution to journalArticle

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