Ulf Ryde's Publications

  1. G. Pettersson, U. Ryde-Pettersson (1987) "A rapid-equilibrium model for the control of the Calvin photosynthesis cycle by cytosolic orthophosphate". Eur. J. Biochem. 169, 423-429; DOI: 10.1111/j.1432-1033.1987.tb13629.x; Open access.

  2. Kvassman, J., G. Pettersson, U. Ryde-Pettersson (1988) "Mechanism of glyceraldehyde-3-phosphate transfer from aldolase to glyceraldehyde-3- phosphate dehydrogenase". Eur. J. Biochem. 172, 427-431; DOI: 10.1111/j.1432-1033.1988.tb13905.x; Open access.

  3. G. Pettersson, U. Ryde-Pettersson (1988) "A mathematical model of the Calvin photosynthesis cycle" Eur. J. Biochem. 175, 661-672; DOI: 10.1111/j.1432-1033.1988.tb14242.x; Open access.

  4. G. Pettersson, U. Ryde-Pettersson (1988) "Effects of metabolite binding to ribulosebisphosphate carboxylase on the activity of the Calvin photosynthesis cycle". Eur. J. Biochem. 177 , 351-355; DOI: 10.1111/j.1432-1033.1988.tb14382.x; Open access.

  5. G. Pettersson, U. Ryde-Pettersson (1989) "Metabolites controlling the rate of starch synthesis in the chloroplast of C3-plants". Eur. J. Biochem.179, 169-172; DOI: 10.1111/j.1432-1033.1989.tb14536.x; Open access.

  6. G. Pettersson, U. Ryde-Pettersson (1989) "On the regulatory significance of inhibitors acting on non-equilibrium enzymes in the Calvin photosynthesis cycle". Eur. J. Biochem. 182 , 373-377; DOI: 10.1111/j.1432-1033.1989.tb14841.x; Open access.

  7. U. Ryde-Pettersson (1989) "A theoretical treatment of damped oscillations in the transient state kinetics of single-enzyme reactions". Eur. J. Biochem. 186, 145-148; DOI: 10.1111/j.1432-1033.1989.tb15188.x; Open access.

  8. G. Pettersson, U. Ryde-Pettersson (1989) "Dependence of the Calvin cycle activity on kinetic parameters for the interaction of non-equilibrium cycle enzymes with their substrates". Eur. J. Biochem. 186 , 683-687; DOI: 10.1111/j.1432-1033.1989.tb15260.x; Open access.

  9. G. Pettersson, U. Ryde-Pettersson (1990) "Model studies of the regulation of the Calvin photosynthesis cycle by cytosolic metabolites". Biomed. Biochim. Acta 49, 723-732.

  10. U. Ryde-Pettersson (1990) "On the mechanistic origin of damped oscillations in biochemical reaction system". Eur. J. Biochem. 194, 431-436; DOI: 10.1111/j.1432-1033.1990.tb15636.x; Open access.

  11. U. Ryde-Pettersson (1991) "Identification of possible two-reactant sources of oscillations in the Calvin photosynthetic cycle and ancillary pathways". Eur. J. Biochem. 198, 613-619; DOI: 10.1111/j.1432-1033.1991.tb16058.x; Open access.

  12. U. Ryde-Pettersson (1992) "Oscillations in coupled enzymic reactions at high concentration of enzyme". Biochim. Biophys. Acta 1119 , 118-12; DOI: 10.1016/0167-4838(92)90380-V.

  13. U. Ryde-Pettersson (1992) "Oscillations in the photosynthetic Calvin cycle - examination of a mathematical model". Acta Chem. Scand. 46, 406-408; DOI: 10.3891/acta.chem.scand.46-0406; Open access. .

  14. U. Ryde-Pettersson (1991) "A theoretical treatment of damped oscillations in biochemical reaction systems with applications to the photosynthetic oscillations". Ph. D. Thesis, University of Lund.

  15. U. Ryde (1994) "The coordination chemistry of the catalytic zinc ion in alcohol dehydrogenase studied by ab initio quantum chemical calculations". Int. J. Quant. Chem. 52, 1229-1243; DOI: 10.1002/qua.560520508. Abstract

  16. U. Ryde (1995) "Molecular dynamic simulations of alcohol dehydrogenase with a four- or five-coordinate catalytic zinc ion". Proteins, Struct. Funct. Genet. 21, 40-56; DOI: 10.1002/prot.340210106. Abstract

  17. U. Ryde (1995) "On the role of Glu-68 in alcohol dehydrogenase", Protein Science 4, 1124-1132; DOI: 10.1002/pro.5560040611; Open access. Abstract

  18. L. Hemmingsen, U. Ryde (1996) "Ab initio calculations of electric field gradients in cadmium complexes". J. Phys. Chem. 100 , 4803-4809; DOI: 10.1021/jp9526410. Abstract

  19. U. Ryde (1996) "The coordination chemistry of the structural zinc ion in alcohol dehydrogenase studied by ab initio quantum chemical calculations". Eur. Biophys. J. 24, 213-221; DOI: 10.1007/BF00205102. Abstract

  20. U. Ryde (1996) "The coordination of the catalytic zinc ion in alcohol dehydrogenase studied by combined quantum chemical and molecular mechanical calculations". J. Comput.-Aided Mol. Design 10, 153-164; DOI: 10.1007/BF00402823. Abstract

  21. U. Ryde, M. H. M. Olsson, K. Pierloot, B. O. Roos (1996) "The cupric geometry of blue copper proteins is not strained". J. Mol. Biol. 261, 586-596. DOI: 10.1006/jmbi.1996.0484

  22. K. Pierloot, J. O. A. De Kerpel, U. Ryde, B. O. Roos (1997) "Theoretical study of the electronic spectrum of plastocyanin". J. Am. Chem. Soc. 119, 218-226; DOI 10.1021/ja962381f. Abstract

  23. R. Lindh, U. Ryde, M. Schütz (1997) "On the significance of the trigger reaction in the action of the calicheamicin anti-cancer drug". Theor. Chem. Acc. 97, 203-210; DOI 10.1007/s002140050254. 

  24. U. Ryde, L. Hemmingsen (1997) "The active-site metal coordination geometry of cadmium-substituted alcohol dehydrogenase. A theoretical interpretation of perturbed angular correlation of gamma ray measurements". J. Biol. Inorg. Chem. 2, 567-579; DOI 10.1007/s007750050171. 

  25. E. Sigfridsson, U. Ryde (1998) "Comparison of methods for deriving atomic charges from the electrostatic potential and moments". J. Comp. Chem. 19, 377-395. DOI 10.1002/(SICI)1096-987X(199803)19:4<377::AID-JCC1>3.0.CO;2-P

  26. M. H. M. Olsson, U. Ryde, B. O. Roos, K. Pierloot (1998) "On the relative stability of tetragonal and trigonal Cu(II) complexes with relevance to the blue copper proteins". J. Biol. Inorg. Chem. , 3, 109-125; DOI 10.1007/s007750050212. Abstract

  27. J. O. A. De Kerpel, K. Pierloot, U. Ryde, B. O. Roos (1998) "Theoretical study of the structural and spectroscopic properties of stellacyanin". J. Phys. Chem. B, 102, 4638-4647; DOI: 10.1021/jp980455z. Abstract

  28. U. Ryde, M. H. M. Olsson, B. O. Roos, K. Pierloot, J. O. A. De Kerpel (1998)" Proteins, Blue Copper: electronic spectra". The Encyclopaedia of Computational Chemistry, P. v. R. Schleyer, N. L. Allinger, T. Clark, J. Gasteiger, P. A. Kollman, H. F. Schaefer III, P. R. Schreiner (Eds.), John Wiley, Sons, Chichester, p. 2255-2270. Book Chapter. Abstract

  29. M. H. M. Olsson, U. Ryde, B. O. Roos (1998) "Quantum chemical calculations of the reorganisation energy of blue copper proteins". Prot. Sci. , 7, 2659-2668; DOI 10.1002/pro.5560071220; Open access.

  30. K. Pierloot, J. O. A. De Kerpel, U. Ryde, M. H. M. Olsson, B. O. Roos (1998) "Relation between the structure and spectroscopic properties of blue copper proteins". J. Am. Chem. Soc., 120, 13156-13166. Free reprint DOI 10.1021/ja982385f

  31. E. Sigfridsson, U. Ryde (1999) "On the significance of hydrogen bonds for the discrimination between CO and O2 by myoglobin". J. Biol. Inorg. Chem., 4, 99-110; DOI 10.1007/s007750050293. 

  32. J. O. A. De Kerpel, U. Ryde (1999) "Protein strain in blue copper proteins studied by free energy perturbations". Proteins, Struct. Funct. Genet., 36, 157-174; DOI 10.1002/(SICI)1097-0134(19990801)36:2<157::AID-PROT3>3.0.CO;2-Y; Open access.

  33. L. Hemmingsen, U. Ryde, R. Bauer (1999) "Nuclear quadrupole interactions in cadmium complexes: Semiempirical and ab initio calculations". Z. Naturforsch. A, 54 a, 422-430; DOI 10.1515/zna-1999-6-713; Open access.

  34. J. O. A. De Kerpel, K. Pierloot, U. Ryde (1999) "Geometric and electronic structure of Co(II)-substituted azurin". J. Phys. Chem. B, 103, 8375-8382; DOI 10.1021/jp991359g.

  35. M. H. M. Olsson, U. Ryde (1999) "The influence of axial ligands on the reduction potential of blue copper proteins". J. Biol. Inorg. Chem., 4, 654-663; DOI 10.1007/s007750050389.

  36. U. Ryde (1999) "Carboxylate binding modes in zinc proteins, a theoretical study". Biophys. J. 77, 2777-2787; DOI 10.102110.1016/S0006-3495(99)77110-9; Open access.

  37. N. Holmberg, U. Ryde, L. Bülow (1999) "Redesign of the coenzyme specificity in L-lactate dehydrogenase from Bacillus stearothermophilus using site-directed mutagenses and media engineering". Prot. Engin. , 12 , 851-856; DOI 10.1093/protein/12.10.851; Open access.

  38. U. Ryde, M. H. M. Olsson, B. O. Roos, K. Pierloot, J. O. A. De Kerpel (2000) "On the role of strain in blue copper proteins". J. Biol. Inorg. Chem., 5, 565-574. DOI 10.1007/s007750000147

  39. U. Ryde, M. H. M. Olsson, K. Pierloot (2001) "The structure and function of blue copper proteins". In Theoretical Biochemistry. Processes and properties of biological systems, L. A. Eriksson, ed., Elsevier, Amsterdam, (Theoretical and Computational Chemistry, vol. 9), 1-56. Book Chapter.

  40. U. Ryde, M. H. M. Olsson (2001) "Structure, strain, and reorganization energy of blue copper models in the protein". Int. J. Quant. Chem., 81, 335-347. Abstract DOI 10.1002/1097-461X(2001)81:5<335::AID-QUA1003>3.0.CO;2-Q

  41. U. Ryde, M. H. M. Olsson, B. O. Roos, A. Borin-Carlos (2001) "A theoretical study of the Cu –cysteine interaction with relevance to the blue copper proteins". Theor. Chem. Acc., 105 , 452-462. DOI 10.1007/s002140000242

  42. E. Sigfridsson, M. H. M. Olsson, U. Ryde (2001) "Inner-sphere reorganization energy of iron–sulphur clusters studied by theoretical methods", Inorg. Chem., 40, 2509-2519. Free reprint DOI 10.1021/ic000752u

  43. E. Sigfridsson, M. H. M. Olsson, U. Ryde (2001) "A comparison of the inner-sphere reorganisation energies of cytochromes, iron-sulphur clusters, and blue copper proteins", J. Phys. Chem. B, 105, 5546-5552. Free reprint; DOI 10.1021/jp0037403 .

  44. M. H. M. Olsson, U. Ryde (2001) "Geometry, reduction potential, and reorganisation energy of the binuclear CuA site, studied by theoretical methods", J. Am. Chem. Soc., 123, 7866-7876. Free reprint DOI 10.1021/ja010315u

  45. E. Sigfridsson, U. Ryde, B. L. Bush (2002) "Restrained point-charge models for disaccharides", J. Comp. Chem., 23, 351-364. DOI 10.1002/jcc.10024

  46. K. P. Jensen, U. Ryde (2002) "The axial N-base has minor influence on Co-C bond cleavage in cobalamins", J. Mol. Struct. (Theochem), 585, 239-255.  DOI: 10.1016/S0166-1280(02)00049-0

  47. U. Ryde, L. Olsen, K. Nilsson (2002) "Quantum chemical geometry optimizations in proteins using crystallographic raw data", J. Comp. Chem., 23, 1058-1070; DOI: 10.1002/jcc.10093.

  48. E. Sigfridsson, U. Ryde (2002) "Theoretical study of the discrimination between O2 and CO by myoglobin", J. Inorg. Biochem., 91 , 101-115; DOI:10.1016/S0162-0134(02)00426-9. 

  49. U. Ryde (2002) "On the role of covalent strain in protein function", in Recent Research Developments in Protein Engineering, 2, pp. 65-91; Research Signpost, Trivandrum. Book Chapter.

  50. K. Nilsson, D. Lecerof, E. Sigfridsson, U. Ryde (2003), "An automatic method to generate force-field parameters for hetero-compounds", Acta Crystallogr. D, 59, 274-289; DOI 10.1107/S0907444902021431.

  51. U. Ryde (2003) "Combined quantum and molecular mechanics calculations on metalloproteins", Curr. Opin. Chem. Biol., 7, 136-142; DOI 10.1016/S1367-5931(02)00016-9. Review article.

  52. L. O. Gerlach, J. S. Jacobsen, K. P. Jensen, M. R. Rosenkilde, R. T. Skerlj, U. Ryde, G. J. Bridger, T. W. Schwartz (2003) "Metal-ion enhanced binding of AMD3100 to Asp-262 in the CXCR4 receptor"  Biochemistry 42, 710-717; DOI: 10.1021/bi0264770

  53. E. Sigfridsson, U. Ryde (2003) "The importance of porphyrin distortions for the ferrochelatase reaction", J. Biol. Inorg. Chem., 8, 273-282; DOI: 10.1007/s00775-002-0413-8.

  54. L. Olsen, J. Antony, U. Ryde, H.-W. Adolph, L. Hemmingsen (2003) "Lactam hydrolysis catalysed by mononuclear metallo-beta-lactamases - a density functional study", J. Phys. Chem. B 107, 2366-2375; DOI: 10.1021/jp0275950.

  55. K. P. Jensen, U. Ryde (2003) "Comparison of the chemical properties of iron and cobalt porphyrins and corrins", ChemBioChem, 4, 413-424; DOI: 10.1002/cbic.200200449.

  56. D. Lecerof, M. N. Fodje, R. A. León, U. Olsson, A. Hansson, E. Sigfridsson, U. Ryde, M. Hansson, S. Al-Karadaghi (2003) "Interaction between two metal binding sites in Bacillus subtilis ferrochelatase", J. Inorg. Biol. Chem., 8, 452-458;  DOI: 10.10 07/s00775-002-0436-1.

  57. K. P. Jensen, U. Ryde (2003) "Importance of proximal hydrogen bonds in haem proteins", Mol. Phys., 101, 2003-2018; DOI 10.1080/0026897031000109383.

  58. U. Ryde, K. Nilsson (2003) "Quantum refinement - a combination of quantum chemistry and protein crystallography", J. Mol. Struct. (Theochem), 632, 259-275; doi: 10.1016/S0166-1280(03)00304-X . Review article.

  59. K. P. Jensen, U. Ryde (2003) "Theoretical prediction of the Co-C bond strength in cobalamins", J. Phys. Chem. A, 107, 7539-7545; DOI: 10.1021/jp027566p; Free reprint.

  60. G. Karlström, R Lindh, P.-Å. Malmqvist, B. O. Roos, U. Ryde, V. Veryazov, P.-O. Widmark, M. Cossi, B. Schimmelpfennig, P. Neogrady, L. Seijo (2003) "MOLCAS: a program package for computational chemistry", Comput. Materials Sci., 28, 222-239; DOI: 10.1021/jp027566p. Review article.

  61. K. P. Jensen, U. Ryde (2003) "Conversion of homocysteine to methionine by methionine synthase: a density functional study", J. Am. Chem. Soc., 125, 13970-13971; DOI: 10.1021/ja034697a; free reprint.

  62. U. Ryde, K. Nilsson (2003) "Quantum chemistry can locally improve protein crystal structures ", J. Am. Chem. Soc., 125, 14232-14233; DOI: 10.1021/ja0365328; free reprint.

  63. B. O. Roos, U. Ryde (2003), "Ab initio methods", in Comprehensive Coordination Chemistry II, From biology to nanotechnology. Vol. 1 Fundamentals, A. B. P. Lever, ed., pp. 519-539. Book Chapter.

  64. P. Rydberg, E. Sigfridsson, U. Ryde (2004) "On the role of the axial ligand in haem proteins - a theoretical study", J. Biol. Inorg. Chem., 9, 203-223; DOI: 10.1007/s00775-003-0515-y.

  65. K. P. Jensen, U. Ryde (2004) "How O2 binds to heme: Reasons for rapid binding and spin inversion", J. Biol. Chem., 279, 14561-14569; DOI: 10.1074/jbc.M314007200; Open access.

  66. Y. Shen, U. Ryde (2004) "The structure of sitting-atop complexes of metalloporphyrins studied by theoretical methods",  J. Inorg. Biochem., 98, 878-895; DOI: 10.1016/j.jinorgbio.2004.01.004.

  67. K. Nilsson, U. Ryde (2004) "Protonation status of protein ligands can be determined by quantum refinement", J. Inorg. Biochem., 98, 1539-1546; DOI:10.1016/j.jinorgbio.2004.06.006.

  68. K. Nilsson, H.-P. Hersleth, T. H. Rod, K. K. Andersson, U. Ryde (2004) "The protonation status of compound II in myoglobin, studied by a combination of experimental data and quantum chemical calculations: quantum refinement", Biophys. J., 87, 3437-3447; doi:10.1529/biophysj.104.041590.

  69. L. Olsen, T. Rasmussen, L. Hemmingsen, U. Ryde (2004) "Binding of benzylpenicillin to metallo-beta-lactamase: a QM/MM study", J. Phys. Chem. B. 108, 17639-17648 ; DOI: 10.1021/jp0482215.

  70. K. P. Jensen, B. O. Roos, U. Ryde (2005) "O2-binding to heme: Electronic structure and spectrum of oxyheme, studied by multiconfigurational methods", J. Inorg. Biochem., 99, 45-54.
    Correction: J. Inorg. Biochem, 99, 978; DOI 10.1016/j.jinorgbio.2005.02.013.

  71. E. S. Ryabova, P. Rydberg, M. Kolberg, E. Harbitz, A.-L. Barra, U. Ryde, K. K. Andersson, E. Nordlander (2005) "A comparative reactivity study of microperoxidases based on hemin, mesohemin and deuterohemin", J. Inorg. Biochem., 99, 852-863; DOI: 10.1016/j.inorgbio.2004.12.020.

  72. Y. Shen, U. Ryde (2005) "Reaction mechanism of porphyrin metallation, studied by theoretical methods", Chem.  Eur. J., 11, 1549-1564; DOI: 10.1002/chem.200400298.

  73. Y.-W. Hsiao, T. Drakenberg, U. Ryde (2005) "NMR structure determination of proteins supplemented by quantum chemical calculations: Detailed structure of the Ca2+ sites in the EGF34 fragment of protein S", J. Biomol. NMR, 31, 97-114; DOI: 10.1007/s10858-004-6729-7.

  74. N. Källrot, K. Nilsson, T. Rasmussen, U. Ryde (2005) "The structure of the catalytic copper site in nitrite reductase, studied by quantum refinement", Intern. J. Quant. Chem., 102, 520-541; DOI: 10.1002/qua.20386.

  75. T. H. Rod, U. Ryde (2005) "Quantum mechanical free energy barrier for an enzymatic reaction", Phys. Rev. Lett., 94, 138302; DOI: 10.1103/PhysRevLett.94.138302.

  76. K. P. Jensen, U. Ryde (2005) "How the Co-C bond is cleaved in coenzyme B12 enzymes, a theoretical study", J. Am. Chem. Soc., 127, 9117-9128; DOI: 10.1021/ja050744i; free reprint.

  77. L. Rulíšek, E. I. Solomon, U. Ryde (2005) "A Combined Quantum and Molecular Mechanical Study of the O2 reductive cleavage in the catalytic cycle of multicopper oxidases", Inorg. Chem., 44, 5612-5628; DOI: 10.1021/ic050092z; Free reprint

  78. T. H. Rod, U. Ryde (2005) "Accurate QM/MM free energy calculations of enzyme reactions: Methylation by catechol O-methyltransferase", J. Chem. Theory Comput., 1, 1240-1251; DOI: 10.1021/ct0501102.

  79. K. P. Jensen, U. Ryde (2005) "Comparison of chemical properties of iron, cobalt, and nickel porphyrins, corrins, and hydrocorphins", J. Porph. Phthalocyanines, 9, 581-606; DOI: 10.1142/S1088424605000691.

  80. Y.-W. Hsiao, U. Ryde (2006) "Interpretation of EXAFS spectra for sitting-atop complexes with the help of computational methods", Inorg. Chim. Acta, 359, 1081-1092; DOI: /10.1016/j.ica.2005.11.036.

  81. H.-P. Hersleth, U. Ryde, P. Rydberg, C. H. Görbitz, K. K. Andersson (2006) "Structures of the high-valent metal-ion haem –oxygen intermediates in peroxidases, oxygenases and catalases", J. Inorg. Biochem., 100, 460-476; DOI: j.jinorgbio.2006.01.018. Review article.

  82. T. H. Rod, P. Rydberg, U. Ryde (2006) "Implicit versus explicit solvent in free energy calculations of enzyme catalysis: Methyl transfer catalyzed by catechol O-methyltransferase", J. Chem. Phys., 124, 174503; DOI: 10.1063/1.2186635.

  83. L. Rulíšek, U. Ryde (2006) "Structure of reduced and oxidised manganese superoxide dismutase - a combined computational and experimental approach", J. Phys. Chem. B, 110, 11511-11518; DOI: 10.1021/jp057295t.

  84. L. Rulíšek, K. P. Jensen, K. Lundgren, U. Ryde (2006) "The reaction mechanism of iron and manganese superoxide dismutases studied by theoretical methods", J. Comput. Chem., 27, 1398-1414; DOI: 10.1002/jcc.20450.

  85. A. V. Gaenko, A. Devarajan, I. V. Tselinskii, U. Ryde (2006) "Structural and photoluminescence properties of excited state intramolecular proton transfer capable compounds - potential emissive and electron transport materials", J. Phys. Chem. A 110, 7935-7942; DOI: 10.1021/jp060646z.

  86. P. Söderhjelm, G. Karlström, U. Ryde (2006) "Comparison of overlap-based models for approximating the exchange-repulsion energy", J. Chem. Phys., 124, 244101; DOI: 10.1063/1.2206182.

  87. P. Söderhjelm, U. Ryde (2006) "Combined computational and crystallographic study of the oxidised states of [NiFe] hydrogenase", J. Mol. Struct. Theochem, 770, 199-219; DOI: 10.1016/j.theochem.2006.06.008.


  88. T. Karlberg, U. Schagerlöf, O. Gakh, S. Park, U. Ryde, M. Lindahl, K. Leath, E. Garman, G. Isaya, S. Al-Karadaghi (2006) "The structure of frataxin oligomers reveal a novel mechanism for the delivery and detoxification of iron", Structure, 14, 1535-1546; doi:10.1016/j.str.2006.08.010.

  89. L. Olsen, P. Rydberg, T. H. Rod, U. Ryde (2006) "Prediction of activation energies for hydrogen abstraction by cytochrome P450", J. Med. Chem., 49, 6489-6499; DOI: 10.1021/jm060551l.

  90. A. Weis, K. Katebzadeh, P. Söderhjelm, I. Nilsson, U. Ryde (2006) “Ligand affinities predicted with the MM/PBSA method: dependence on the simulation method and the force field”, J. Med. Chem., 49, 6596-6606; DOI: 10.1021/jm0608210; free reprints.

  91. Y.-W. Hsiao, Y. Tao, J. E. Shokes, R. A. Scott, U. Ryde (2006) "EXAFS structure refinement supplemented by computational chemistry", Phys. Rev. B, 74, 214101; DOI:  10.10.1103/PhysRevB.74.214101.

  92. J. Chalupský, F. Neese, E. I. Solomon,U. Ryde, L. Rulíšek (2006) "Multireference ab initio calculations on reaction intermediates of multicopper oxidases",  Inorg. Chem., 45, 11051-11059; DOI: 10.1021/ic0619512; free reprints.

  93. J. Heimdal, K. P. Jensen, A. Devarajan, U. Ryde (2007), "The role of axial ligands for the structure and function of chlorophylls", J. Biol. Inorg. Chem. 12, 49-61; DOI: 10.1007/s00775-006-0164-z.

  94. U. Ryde (2007) "Accurate metal-site structures in proteins obtained by combining experimental data and quantum chemistry", Dalton Trans., 2007, 607-625, DOI: 10.1039/b614448a; pdf. Review article.

  95. K. P. Jensen, B. O. Roos, U. Ryde (2007) "Performance of density functionals for first row transition metal systems", J. Chem. Phys, 126, 014103; DOI: 10.1039/b614448a.

  96. U. Ryde, Y.-W. Hsiao, L. Rulíšek, E. I. Solomon (2007) "Identification of the peroxy adduct in multicopper oxidases by a combination of computational chemistry and extended X-ray absorption fine-structure measurements", J. Am. Chem. Soc., 129, 726-727; DOI: 10.1021/ja062594g; free reprints.

  97. P. Söderhjelm, J. W. Krogh, G. Karlström, U. Ryde, R. Lindh (2007) "Assessment of LoProp and MpProp molecular mechanics potentials for amino acids", J. Comput. Chem., 28, 1083-1090; DOI: 10.1002/jcc.20632.

  98. P. Rydberg, T. H. Rod, L. Olsen, U. Ryde (2007) "Dynamics of water molecules in the active-site cavity of human cytochromes P450", J. Phys. Chem. B 111, 5445-5457; DOI: 10.1021/jp070390c; free reprints.

  99. C. Greco, M. Bruschi, L. Di Gioia , U. Ryde (2007) "A QM/MM investigation of the activation and catalytic mechanism of Fe-only hydrogenases", Inorg. Chem., 46, 5911-5921; DOI: 10.1021/ic062320a.

  100. C. Greco, M. Bruschi, J. Heimdal, P. Fantucci, L. Di Gioia , U. Ryde (2007) "Structural insights into the active-ready form of the Fe-only hydrogenas and mechanistic details of the inhibition by carbon monoxide", Inorg. Chem., 46, 7256-7258;  DOI: 10.1021/ic701051h.

  101. P. Rydberg, L. Olsen, P.-O. Norrby, U. Ryde (2007) "A general transition-state force field for cytochrome P450 hydroxylation", J. Chem. Theory Comput., 3, 1765-1773;  DOI: 10.1021/ct700110f; free reprints (the 15th most accessed article in JCTC the month after publication).

  102. J. Kongsted, U. Ryde, J. Wydra, J. H. Jensen (2007) "Prediction and rationalization of the pH-dependence of activity and stability of family 11 xylanases", Biochemistry, 46, 13581-13592; DOI: 10.1021/bi7016365.

  103. K P. Jensen, P. Rydberg, J. Heimdal, U. Ryde (2008) "A comparison of the tetrapyrrole cofactors in nature and their tuning by axial ligands" , in Computational modeling for homogeneous and enzymatic catalysis, K. Morokuma, J. Musaev, eds., Wiley-VCH, Weinheim, pp. 27-56. Book Chapter.

  104. P. Söderhjelm, A. Öhrn, U. Ryde, G. Karlström, "Accuracy of typical approximations in classical models of intermolecular polarization", J. Chem. Phys., 128 (2008) 014102; DOI: 10.1063/1.2814240.

  105. J. Ballmann, S. Dechert, E. Bill, U. Ryde, F. Meyer, "Secondary bonding interactions in biomimetic [2Fe2S] clusters", Inorg. Chem., 47 (2008) 1586-1596; DOI: 10.1021/ic702095a.

  106. J. Heimdal, P. Rydberg, U. Ryde (2008) " Protonation of the proximal histidine ligand in haem peroxidases", J. Phys. Chem. B., 112, 2501-2510.; DOI: 10.1021/jp710038s; free reprints.

  107. P. Rydberg, S. M. Hansen, J. Kongsted, P.-O. Norrby, L. Olsen, U. Ryde (2008) "Transition-state docking of flunitrazepam and progesterone in cytochrome P450", J. Chem. Theor. Comput., 4, 673-681; DOI: 10.1021/ct700313j; free reprints.

  108. H.-P. Hersleth, Y.-W. Hsiao, U. Ryde, C. H. Görbitz, K. K. Andersson (2008) "The crystal structure of peroxymyoglobin generated through radiolysis of myoglobin compound III during data collection", Biochem. J., 412, 257-264; DOI: 10.1042/BJ20070921.

  109. A. Devarajan, A. V. Gaenko, U. Ryde, "Effect of covalent links on the structure, spectra, and redox properties of myeloperoxidase - a density functional study", J. Inorg. Biochem., 2008, 102, 1549-1557; DOI: 10.1016/j.jinorgbio.2008.01.031.

  110. P. Rydberg, U. Ryde, L. Olsen, "Sulfoxide, sulfur, and nitrogen  oxidation and dealkylation by cytochrome P450", J. Chem. Theory Comput., 2008, 4, 1369-1377; DOI: 10.1021/ct800101v.

  111. M. Kaukonen, P. Söderhjelm, J. Heimdal, U. Ryde (2008) "Proton transfer at metal sites in proteins studied by quantum mechanical free-energy perturbations", J. Chem. Theory Comput. 4, 985-1001; DOI: 10.1021/ct700347h; free reprints; The cover image for the  J. Chem. Theory Comput. Vol. 4, issue 6 was taken from this article.

  112. M. Bruschi, C. Greco, G. Zampella, U. Ryde, C. J. Pickett, L. De Gioia (2008) "A DFT investigation on structural and redox properties of a synthetic Fe6S6 assembly closely related to the [FeFe]-hydrogenase active site", Comptes Rendus Chimie, 11, 834-841; DOI: 10.1016/j.crci.2008.04.010.

  113. H.-P. Hersleth, Y.-W. Hsiao, U. Ryde, C. H. Görbitz, K. K. Andersson (2008) "The influence of X-rays on the structural studies of peroxide-derived myoglobin intermediates", Chem. Biodivers., 5, 2067-2089; DOI: 10.1002/cbdv.200890189.

  114. M. Kaukonen, P. Söderhjelm, J. Heimdal, U. Ryde (2008) "A QM/MM-PBSA method to estimate free energies for reactions in proteins", J. Phys. Chem. B, 2008, 112, 12537-12548; DOI: 10.1021/jp802648k; free reprints.

  115. J. Ballmann, A. Albers, S. Demeshko, S. Dechert, E. Bill, E. Bothe, U. Ryde, F. Meyer (2008), "A Synthetic Analogue of Rieske-Type [2Fe 2S] Cluster", Angew. Chem., Intern. Ed., 2008, 47, 9537-9541 (120, 9680); DOI: 10.1002/anie.200803418. The inside cover illustration of the 2008-47/49 issue was selected from this paper.

  116. P. Rydberg, U. Ryde, L. Olsen (2008) "Prediction of activation energies for aromatic oxidation by cytochrome P450", J. Phys. Chem. A, 2008, 112, 13058-13065; DOI: 10.1021/jp803854v.

  117. J. Kongsted, U. Ryde (2009) "An improved method to predict the entropy term with the MM/PBSA approach", J. Comput. Aided Mol Design, 23, 63-71; DOI: 10.1007/s10822-008-9238-z.

  118. P. Söderhjelm, U. Ryde (2009) "How accurate can a force field become? - A polarizable multipole model combined with fragment-wise quantum-mechanical calculations" J. Phys. Chem. A,  113, 617-627; DOI: 10.1021/jp8073514.

  119. K P. Jensen, U. Ryde (2009) "Cobalamins uncovered by modern electronic structure calculations", Coord. Chem. Rev., 253. 769-778; Review article; DOI:  10.1016/j.ccr.2008.04.015

  120. P. Söderhjelm, U. Ryde (2009) "Conformational dependence of charges in protein simulations", J. Comput. Chem., 30, 750-760; DOI: 10.1002/jcc.21097.

  121. P. Söderhjelm, C. Husberg, A. Strambi, M. Olivucci, U. Ryde (2009) "Protein influence on electronic spectra modelled by multipoles and polarisabilities", J. Chem. Theory Comput. 5, 649-658; DOI: 10.1021/ct700347h.

  122. M. Bruschi, C. Greco, M. Kaukonen, P. Fantucci, U. Ryde, L. De Gioia (2009) "Role of the [2Fe]H subcluster environment on the electronic and structural properties of key intermediate species formed in the catalytic cycle of [FeFe] hydrogenases", Angew. Chem. Int. Ed., 48, 3503-3506; DOI: 10.1002/anie.200900494.

  123. M. Srnec, F. Aquilante, U. Ryde, L. Rulíšek (2009) "Reaction mechanism of manganese superoxide dismutase studied by combined quantum and molecular mechanical calculations and multiconfigurational methods", J. Phys. Chem. B, 113, 6074-6086; DOI: 10.1021/jp810247u

  124. J. Kongsted, P. Söderhjelm, U. Ryde (2009) "How accurate are continuum solvation models for drug-like molecules?", J. Comp.-Aided Mol. Design, 23, 395-409;  DOI: 10.1007/s10822-009-9271-6

  125. P. Söderhjelm, F. Aquilante, U. Ryde (2009)  "Calculation of Protein-Ligand Interaction Energies by a Fragmentation Approach Combining High-Level Quantum Chemistry with Classical Many-Body Effects", J. Phys. Chem., B, 113, 11085-11094; DOI: 10.1021/jp810551h.

  126. C. Diehl, S. Genheden, K. Modig, U. Ryde, M. Akke (2009) "Conformational entropy changes upon lactose binding to the carbohydrate recognition domain of galectin-3", J. Biomol. NMR, 45, 157-169, DOI: 10.1007/s10858-009-9356-5.

  127. U. Ryde (2009) "Quantum mechanical/molecular mechanical (QM/MM) methods and applications in bioinorganic chemistry", in Computational inorganic and bioinorganic chemistry, E. I. Solomon, R. B. King, R. A. Scott, eds. J. Wiley, Sons, Ltd.  Chichester, UK, pp. 33-42. Book Chapter.

  128. K. Starke, U. Ryde, C. Schulzke "Which functional groups of the molybdopterin ligand should be considered when modeling the active sites of the molybdenum and tungsten cofactors? - a DFT study", J. Biol. Inorg. Chem., 2009, 14, 1053-1064; DOI: 10.1007/s00775-009-0548-y.

  129. L. Hu, J. Eliasson, J. Heimdal, U. Ryde (2009) "Do quantum mechanical energies calculated for small models of protein active sites converge?", J. Phys. Chem. A, 113, 11793–11800; DOI: 10.1021/jp9029024; free reprints.

  130. G. Zoppellaro, K. L. Bren, A. A. Ensign, E. Harbitz, R. Kaur, H.-P. Hersleth, U. Ryde, L. Hederstedt, K. K. Andersson (2009) "Studies of ferric heme proteins with highly anisotropic/highly axial low spin (S = 1/2) electron paramagnetic resonance signals with two histidines or histidine and methionine axial Fe coordination", Biopol., 91, 1064-1082; DOI:10.1002/bip.21267.

  131. Y. Wang, Y. Shen, U. Ryde (2009) "QM/MM study of the insertion of metal ions into protoporphyrin IX by ferrochelatase", J. Inorg. Biochem. 103, 1680-1686; DOI: 10.1016/j.jinorgbio.2009.09.013.

  132. U. Ryde (2009) "Rubus sect. Corylifolii in the province of Halland, SW Sweden", Svensk Bot. Tidskr. 103, 279-300; pdf; Rubus.

  133. M. G. G. Fuchs, F. Meyer, U. Ryde (2010) "A combined computational and experimental investigation of the [2Fe-2S] cluster in biotin synthase", J. Biol. Inorg. Chem., 15. 203-212; DOI: 10.1007/s00775-009-0585-6.

  134. S. Genheden, U. Ryde (2010) "How to obtain statistically converged MM/GBSA results", J. Comput. Chem., 31, 837-846; DOI: 10.1002/jcc.21366.

  135. P. Söderhjelm, J. Kongsted, S. Genheden, U. Ryde (2010) "Estimates of ligand-binding affinities supported by quantum mechanical methods", Interdiscip. Sci. Comput. Life Sci., 2, 21-37; DOI: 10.1007/s12539-010-0083-0. Review article.

  136. U. Ryde, C. Greco, L. De Gioia (2010) "Quantum refinement of [FeFe] hydrogenase indicates a dithiomethylamine ligand", J. Am. Chem. Soc., 132, 4512-4513; DOI: 10.1021/ja909194f;  free reprint.

  137. U. Ryde (2010) "Genetic analysis shows that Rubus vikensis is a distinct species with a disjunct distribution" Nordic J. Bot. 28, 246-250; DOI: 10.1111/j.1756-1051.2009.00663.x; Rubus.

  138. M. Bruschi, C. Greco, L. Bertini, P. Fantucci, U. Ryde, L. De Gioia (2010) Functionally relevant interplay between the Fe4S4 cluster and CN- ligands in the active site of [Fe,Fe] hydrogenases. J. Am. Chem. Soc., 132, 4992-4993; DOI: 10.1021/ja1008773.

  139.  P. Söderhjelm, J. Kongsted, U. Ryde (2010) "Ligand affinities estimated by quantum chemical calculations", J. Chem. Theory Comput., 6, 1726-1737; DOI: 10.1021/ct9006986; free reprints.

  140. S. Vancoillie, J. Chalupský, U. Ryde, E. I. Solomon, K. Pierloot, F. Neese, L. Rulíšek (2010) "Multireference ab initio calculations of g tensors for trinuclear copper clusters in multicopper oxidases", J. Phys. Chem. B, 114. 7692-7702; DOI: 10.1021/jp103098r.

  141. S. Genheden, T. Luchko, S. Gusarov, A. Kovalenko, U. Ryde (2010) "An MM/3D-RISM approach for ligand-binding affinities", J. Phys. Chem. B, 114, 8505-8516; DOI: 10.1021/jp101461s; free reprints.

  142. M. G. G. Fuchs, S. Dechert, S. Demeshko, U. Ryde, F. Meyer (2010) "A five-coordinate [2Fe-2S] cluster" Inorg. Chem., 49, 5853-5858; DOI: 10.1021/ic902559n.

  143. S. Genheden, C. Diehl, M. Akke, U. Ryde (2010) "Starting-condition dependence of order parameters derived from molecular dynamics simulations" J. Chem. Theory Comput., 6, 2176-2190; DOI: 10.1021/ct900696z; free reprints.

  144. C. Diehl, O. Engström, T. Delaine, M. Håkansson, S. Genheden, K. Modig, H. Leffler, U. Ryde, U. J. Nilsson, M. Akke (2010) "Protein flexibility and conformational entropy in ligand design targeting the carbohydrate recognition domain of galectin-3", J. Am. Chem. Soc., 132, 14577-14589; DOI: 10.1021/ja105852y, Open access; pdf; chosen for JACS select.

  145. S. Genheden, J. Kongsted, P. Söderhjelm, U. Ryde (2010) "Nonpolar solvation free energies of protein–ligand complexes", J. Chem. Theory Comput., 6, 3558-3568; DOI 10.1021/ct100272s; free reprints

  146. U. Ryde, G. Werlemark (2010) "Rubus sordirosanthus in Halland, southwest Sweden", Svensk Bot. Tidskr. 104, 405-413; pdf; Rubus.

  147. S. Genheden, U. Ryde "A comparison of different initialization protocols to obtain statistically independent molecular dynamics simulations" J. Comput. Chem. 2011, 32, 187-195; DOI 10.1002/jcc.21564.

  148. M. Srnec, U. Ryde, L. Rulíšek "Reductive cleavage of the O-O bond in multicopper oxidases: a QM/MM and QM study" Faraday Discuss. 2011, 148, 41-51; DOI 10.1039/c004476h; pdf. 

  149. T. Rocha-Rinza, T. Sneskov, O. Christiansen, U. Ryde, J. Kongsted "Unraveling the similarity of the photoabsorption of the deprotonated p-coumaric acid in gas phase and within the photoactive yellow protein", Phys. Chem. Chem. Phys. 2011, 13, 1585-1589; DOI 10.1039/C0CP01075H; pdf.

  150. L. Hu, P. Söderhjelm, U. Ryde "On the convergence of QM/MM energies" J. Chem. Theory Comput., 2011, 7, 761-777; DOI 10.1021/ct100530r; free reprints.

  151. C. Greco, M. Bruschi, P. Fantucci, U. Ryde, L. De Gioia "Isocyanide in biochemistry? A theoretical investigation of the electronic effects and the energetics of cyanide ligand protonation in [FeFe]-hydrogenases", Chem. Eur. J., 2011, 17, 1954-1965; DOI 10.1002/chem.201001493.

  152. C. Greco, A. Silakov, M. Bruschi, U. Ryde, L. Di Gioia, W. Lubitz "Magnetic properties of [FeFe]-hydrogenases: A theoretical investigation based on extended QM and QM/MM models of the H-cluster and its surroundings" Eur. J. Inorg. Chem., 2011, 7, 1043-1049; DOI 10.1002/ejic.201001058.

  153. S. Genheden, I. Nilsson, U. Ryde "Binding affinities of factor Xa inhibitors estimated by thermodynamic integration and MM/GBSA", J. Chem. Inf. Model., 2011, 51, 947-958; DOI 10.1021/ci100458f; free reprints.

  154. P. Söderhjelm, J. Kongsted, U. Ryde "Conformational dependence of isotropic polarisabilities" J. Chem. Theory Comput., 2011, 7, 1404-1414; DOI 10.1021/ct100714e; free reprints. 

  155. L. Yu, C. Greco, M. Bruschi, U. Ryde, L. De Gioia, M. Reiher "Targeting intermediates of [FeFe]-hydrogenase by CO and CN vibrational signatures", Inorg. Chem., 2011, 50, 3888-3900; DOI 10.1021/ic102039z. 

  156. L. Hu, U. Ryde "Comparison of methods to obtain force-field parameters for metal sites" J. Chem. Theory Comput., 2011, 7, 2452-2463; DOI 10.1021/ct100725a; The 8th most accessed article in the journal during Q3-2011. 

  157. S. Genheden, P. Mikulskis, L. Hu, J. Kongsted, P. Söderhjelm, U. Ryde "Accurate predictions of nonpolar solvation free energies require explicit consideration of binding site hydration", J. Am. Chem. Soc., 2011, 133, 13081-13092; DOI 10.1021/ja202972m.; Summarised and commented in Computational Chemistry Highlights.

  158. A. Ciancetta, S. Genheden, U. Ryde "A QM/MM study of the binding of RAPTA ligands to cathepsin B" J. Comput.-Aided Mol. Des., 2011, 25, 729-742; DOI 10.1007/s10822-011-9448-7.

  159. C. Greco, P. Fantucci, U. Ryde, L. De Gioia "Fast generation of broken-symmetry states in a large system including multiple iron–sulfur assemblies: Investigation of QM/MM energies, cluster charges, and spin populations", Intern. J. Quant. Chem, 2011, 111, 3949-3960; DOI 10.1002/qua.22849.

  160. U. Ryde, R. A. Mata, S. Grimme "Does DFT-D estimate accurate energies for the binding of ligands to metal complexes?" Dalton Trans., 2011, 40, 11176-11183; DOI 10.1039/C1DT10867K; pdf.

  161. Greco, C.; Bruschi, M.; Fantucci, P.; Ryde, U.; De Gioia, L. "Probing the effects of one-electron reduction and protonation on the electronic properties of the Fe–S clusters in the active-ready form of [FeFe]-hydrogenases. A QM/MM investigation". Chem. Phys. Chem., 2011, 12, 3376-3382; DOI 10.1002/cphc.201100498.

  162. C. Greco, M. Bruschi, P. Fantucci, U. Ryde, L. De Gioia "Mechanistic and physiological implications of the interplay among iron–sulfur clusters in [FeFe]-hydrogenases. A QM MM perspective", J. Am. Chem. Soc., 2011, 133, 18742-18749; DOI 10.1021/ja205542k.

  163. Hu, L.; Farrokhnia, M.; Heimdal, J.; Shleev, S.; Rulíšek, L.; Ryde, U. "Reorganisation energy for internal electron transfer in multicopper oxidases", J. Phys. Chem. B, 2011, 115, 13111-13126; DOI 10.1021/jp205897z.

  164. S. Genheden, U. Ryde "Comparison of the efficiency of the LIE and MM/GBSA methods to calculate ligand-binding energies", J. Chem. Theory Comput., 2011, 7, 3768-3778; DOI 10.1021/ct200163c.

  165. J. Heimdal, M. Kaukonen, M. Srnec, L. Rulíšek, U. Ryde "Reduction potentials and acidity constants of Mn superoxide dismutase calculated by QM/MM free-energy methods" Chem. Phys. Chem., 2011, 12, 3337-3347; DOI 10.1002/cphc.201100339.

  166. U. Ryde "Arguments for a narrow species concept in Rubus sect. Corylifolii" Nordic J. Bot., 2011, 29, 708-721; DOI 10.1111/j.1756-1051.2011.01203.x; Rubus.

  167. Saraboji, K.; Håkansson, M.; Genheden, S.; Diehl, C.; Qvist, J.; Weininger, U.; Nilsson, U. J.; Leffler, H.; Ryde, U.; Akke, M.; Logan, D. T. "The carbohydrate-binding site in galectin-3 is pre-organized to recognize a sugar-like framework of oxygens: implications for drug design" Biochem., 2012, 51, 296-306; DOI 10.1021/bi201459p, Open access; pdf.

  168. S. Genheden, P. Söderhjelm, U. Ryde (2012) "Transferability of conformational dependent charges from protein simulations" Int. J. Quant. Chem., 112, 1768-1785; DOI 10.1002/qua.22967.

  169. Mikulskis, P.; Genheden, S.; Wichmann, K.; Ryde, U. (2012) "A semiempirical approach to ligand-binding affinities: Dependence on the Hamiltonian and corrections" J. Comput. Chem. 33, 1179-1189; DOI 10.1002/jcc.22949.

  170. P. Söderhjelm, S. Genheden, U. Ryde (2012) "Quantum mechanics in structure-based ligand design", in Protein-ligand interactions, H. Gohlke, ed., Methods and principles in medicinal chemistry vol. 53. Wiley-VCH Verlag, Weinheim, pp. 121-143. Book Chapter.

  171. Genheden, S.; Ryde, U. "Will molecular dynamics simulations of proteins ever reach equilibrium?" Phys. Chem. Chem. Phys., 2012,14, 8662-8677; DOI 10.1039/C2CP23961B; pdf.

  172. Genheden, S.; Ryde, U. "Comparison of end-point continuum-solvation methods for the calculation of protein–ligand binding free energies", Proteins, 2012, 80, 1326-1342; DOI 10.1002/prot.24029.

  173. Genheden, S.; Ryde, U. "Improving efficiency of protein–ligand binding free-energy calculations by system truncation", J. Chem. Theory Comput., 2012, 8, 1449-1458; DOI 10.1021/ct200853g.

  174. Mikulskis, P.; Genheden, S.; Rydberg, P.; Sandberg, L.; Olsen, L.; U. Ryde "Binding affinities of the SAMPL3 trypsin and host-guest blind tests estimated with the MM/PBSA and LIE methods", J. Comput.-Aided Mol. Design, 2012, 26, 527-541; DOI 10.1007/s10822-011-9524-z.

  175. S. Shleev, C. Reimann, V. Andoralov, M. Falk, T. Ruzgas, M. Srnec, U. Ryde, L. Rulíšek "On the possibility of uphill intramolecular electron transfer in multicopper oxidases: electrochemical and quantum chemical study of bilirubin oxidase", Electroanalysis, 2012, 24, 1524-1540; DOI 10.1002/elan.201200188.

  176. Rydberg, P.; Olsen, L.; Ryde, U. "Quantum-mechanical studies of reactions performed by cytochrome P450 enzymes" Curr. Inorg. Chem., 2012, 2, 292-315. Review article.

  177. Heimdal, J.; Ryde, U. "Convergence of QM/MM free-energy perturbations based on molecular-mechanics or semiempirical simulations", Phys. Chem. Chem. Phys., 2012, 14, 12592-12604; DOI 10.1039/C2CP41005B; pdf.

  178. Uranga, J.; Mikulskis, P.; Genheden, S.; Ryde, U. "Can the protonation state of histidine residues be determined from molecular dynamics simulations?", Comput. Theor. Chem., 2012, 1000, 75-84; DOI 10.1016/j.comptc.2012.09.025.

  179. 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" J. Chem. Inf. Model. , 2012, 52 2079-2088; DOI 10.1021/ci3001919.

  180. Rulíšek, L.; Ryde, U. "Theoretical studies of the active-site structure, spectroscopic and thermodynamic properties, and reaction mechanism of multicopper oxidases", Coord. Chem. Rev., 2013, 257, 445-458; Review article. DOI 10.1016/j.ccr.2012.04.019.

  181. L. Hu, P. Söderhjelm, U. Ryde "Accurate reaction energies in proteins obtained by combining QM/MM and large QM calculations" J. Chem. Theory Comput. 2013, 9, 640-649; DOI 10.1021/ct3005003.

  182. X. Li, E. M. Sproviero, U. Ryde, V. S. Batista, G. Chen, "Theoretical EXAFS studies of a model of the oxygen-evolving complex of photosystem II obtained with the quantum cluster approach", Intern. J. Quant. Chem., 2013, 113, 474-478; DOI 10.1002/qua.24143.

  183. M. Irani, U. Törnvall, S. Genheden, M. Wittrup Larsen, R. Hatti-Kaul, U. Ryde, "Amino acid oxidation of Candida antarctica lipase B studied by molecular dynamics simulations and site-directed mutagenesis" Biochemistry, 2013, 52, 1280-1289; DOI 10.1021/bi301298m.

  184. Li, J.-L.; Mata, R. A.; Ryde, U. "Large density-functional and basis-set effects for the DMSO reductase catalyzed oxo-transfer reaction", J. Chem. Theory Comput., 2013, 9, 1799-1807; DOI : 10.1021/ct301094r.

  185. Godschalk, F.; Genheden, S.; Söderhjelm, P.; Ryde, U. "Comparison of MM/GBSA calculations based on explicit and implicit solvent simulations" , Phys. Chem. Chem. Phys., 2013, 15, 7731-7739; DOI : 10.1039/C3CP00116D; pdf.

  186. Husberg, C.; Ryde, U. "How are hydrogen-bonds modified by metal binding?", J. Biol. Inorg. Chem., 2013, 18, 499-522; DOI : 10.1007/s00775-013-0996-2.

  187. Van Severen, M.-C.; Ryde, U.; Parisel, O.; Piquemal, J.-P. "Understanding the chemistry of lead at a molecular level: the Pb(II) 6s6p lone pair can be bisdirected in proteins", J. Chem. Theory Comput.; 2013, 9, 2416-2424; DOI: 10.1021/ct300524v.

  188. Sumner, S.; Söderhjelm, P.; Ryde, U., "Effect of geometry optimisations on QM-cluster and QM/MM studies of reaction energies in proteins", J. Chem. Theory Comput., 2013, 9, 4205-4214; DOI: 10.1021/ct400339c.

  189. S. P. de Visser, M. G. Quesne, B. Martin, P. Comba, U. Ryde (2014) "Computational modelling of oxygenation processes in enzymes and biomimetic model complexes", Chem. Commun., 50, 262-282; DOI: 10.1039/c3cc47148a; pdf. Review article.

  190. Hedegård, E. D.; Knecht, S.; Kongsted, J.; Ryde, U.; Saue, T. (2014) "Can 57Fe Mössbauer isomer shifts be calculated accurately without fitting? Isomer shifts for [Fe]-Hydrogenase Intermediates" Phys. Chem. Chem. Phys., 16, 4853-4863; DOI: 10.1039/c3cp54393; pdf.

  191. Genheden, S.; Akke, M.; U. Ryde (2014) "Conformational entropies and order parameters: convergence, reproducibility, and transferability", J. Chem. Theory Comput., 10, 432-438; DOI: 10.1021/ct400747s; Open access; pdf.

  192. Oksanen, E.; Blakeley, M.; El-Hajji, M.; Ryde, U.; Castro, B.; Budayova-Spano, M. (2014) "The neutron structure of urate oxidase resolves a long-standing mechanistic conundrum and reveals unexpected changes in protonation" PLOS One. 9, e86651; DOI 10.1371/journal.pone.0086651; Open access; pdf.

  193. Sun, X.; Geng, C.; Huo, R.; Ryde, U.; Bu, X.; Li, J.-L. (2014) "Large equatorial ligand effects on C-H bond activation by non-heme FeIVO complexes", J. Phys. Chem. B, 118, 1493-1500; DOI: 10.1021/jp410727r.

  194. M. G. Delcey, K. Pierloot, Q. M. Phung, S. Vancoillie, R. Lindh, U. Ryde  (2014) "Accurate calculations of geometries and singlet-triplet energy differences for active-site models of [NiFe] hydrogenase", Phys. Chem. Chem. Phys., 16, 7927-7938; DOI: 10.1039/C4CP00253A; Open access; pdf.

  195. P. Mikulskis, S. Genheden, U. Ryde (2014) "Effect of explicit water molecules for ligand-binding affinities calculated with the MM/GBSA approach", J. Mol. Model., 20, 2273; DOI: 10.1007/s00894-014-2273-x.

  196. P. Mikulskis, D. Cioloboc, M. Andrejić, S. Khare, J. Brorsson, S. Genheden, R. A. Mata, P. Söderhjelm, U. Ryde (2014) "Free-energy perturbation and quantum mechanical study of SAMPL4 octa-acid host-guest binding energies", J. Comp.-Aided Mol. Design, 28, 375-400; DOI: 10.1007/s10822-014-9739-x.

  197. U. Ryde (2014) "A fundamental view of enthalpy–entropy compensation" Med. Chem. Commun., 5, 1324-1336; DOI: 10.1039/C4MD00057A; Open access; pdf.

  198. M.-C. van Severen, M. Andrejić, J.-L. Li, K. Starke, R. A. Mata, E. Nordlander, U. Ryde (2014) "A quantum-mechanical study of the reaction mechanism of sulfite oxidase", J. Biol. Inorg. Chem., 19, 1165-1179; DOI: 10.1007/s00775-014-1172-z.

  199. M. Andrejić, U. Ryde, R. A. Mata, P. Söderhjelm (2014) "Coupled-cluster interaction energies for 200-atom host-guest systems", Chem. Phys. Chem., 15, 3270-3281; DOI 10.1002/cphc.201402379.

  200. P. Mikulskis, S. Genheden, U. Ryde (2014) "A large-scale test of free-energy simulation stimates of protein-ligand binding affinities", J. Chem. Inf. Model., 54, 2794-2806; DOI: 10.1021/ci5004027; Open Access; pdf.

  201. J.-L. Li, U. Ryde (2014) "Comparison of the active-site design of molybdenum oxo-transfer enzymes by quantum-mechanical calculations" Inorg. Chem., 53, 11913-11924; DOI: 10.1021/ic5010837.

  202. X. Li, P. E. M. Siegbahn, U. Ryde (2015) "A simulation of the isotropic EXAFS spectra for the S2 and S3 structures of the oxygen evolving complex in photosystem II." Proc. Natnl. Ac. Sci. USA, 112, 3979-3984; DOI: 10.1073/pnas.1422058112; pdf.

  203. E. D. Hedegård, J. Kongsted, U. Ryde (2015) "Multiscale modelling of the active site of [Fe]-hydrogenase: The H2 binding site in open and closed protein conformations", Angew. Chem., 54, 6246-6250 DOI: 10.1002/anie.201501737.

  204. S. Genheden, U. Ryde (2015) "The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities" Expert Opinion Drug Discov., 10, 449-461; DOI: 10.1517/17460441.2015.1032936; Open Access; pdf. Review article.

  205. J. Li, M. Andrejić, R. A. Mata, U Ryde (2015) "A computational comparison of oxygen atom transfer catalyzed by DMSO reductase with Mo and W", Eur. J. Inorg. Chem., 2015, 3580-3589; DOI: 10.1002/ejic.201500209.

  206. J. Li, M. Farrokhnia, L. Rulíšek, U. Ryde (2015) "Catalytic cycle of multicopper oxidases studied by combined quantum- and molecular-mechanical free-energy perturbation methods", J. Phys. Chem. B, 119, 8268-8284; DOI 10.1021/acs.jpcb.5b02864; free reprints.

  207. S. Genheden, U. Ryde, P. Söderhjelm (2015) "Binding affinities by alchemical perturbation using QM/MM with a large QM system and polarizable MM model", J. Comput. Chem. 36, 2114-2124; DOI 10.1002/jcc.24048.

  208. G. Dong, U. Ryde (2016) "Protonation states of intermediates in the reaction mechanism of [NiFe] hydrogenase studied by computational methods", J. Biol. Inorg. Chem., 21, 383-394; DOI 10.1007/s00775-016-1348-9.

  209. U. Ryde, P. Söderhjelm (2016) "Ligand-binding affinity estimates supported by quantum-mechanical methods", Chem. Rev. 116, 5520-5566; DOI 10.1021/acs.chemrev.5b00630; Open Access. Review article.

  210. M. A. Olsson, P. Söderhjelm, U. Ryde (2016) "Converging ligand-binding free energies obtained with free-energy perturbations at the quantum mechanical level" J. Comput. Chem., 37, 1589-1600; DOI 10.1002/jcc.24375; Open Access.

  211. S. Jafari, U. Ryde, M. Irani (2016) "Catalytic mechanism of human glyoxalase I studied by quantum-mechanical cluster calculations". J. Mol. Catal. B 131, 18-30; DOI: 10.1016/j.molcatb.2016.05.010; submitted version.

  212. U. Ryde (2016) QM/MM calculations on proteins. Meth. Enz., 577, 119-158; DOI: 10.1016/bs.mie.2016.05.014. Book Chapter.

  213. U. Ryde, G. Dong, J. Li, M. Feldt, R. A. Mata (2016) "Computational studies of molybdenum and tungsten enzymes" In Molybdenum and Tungsten Enzymes, Eds. R. Hille, M. Kirk, C. Schulzke, RSC Metallobiology series no. 7; pp. 275-321; DOI: 10.1039/9781782628842-00275. Book Chapter.

  214. M. Misini Ignjatović, O. Caldararu, G. Dong, C. Muñoz-Gutierrez, F. Adasme-Carreño, U. Ryde, (2016) "Binding-affinity predictions of HSP90 in the D3R Grand Challenge 2015 with docking, MM/GBSA, QM/MM, and free-energy simulations", J. Comp.-Aided Mol. Design, 30, 707-730; DOI 10.1007/s10822-016-9942-z; Open Access.

  215. A. Fouda, U. Ryde (2016) "Does the DFT self-interaction error affect energies calculated in proteins with large QM systems?" J. Chem. Theory Comput., 12, 5667-5679; DOI 10.1021/acs.jctc.6b00903; Open Access.

  216. G. Dong, U. Ryde (2016) "O2 Activation in Salicylate 1,2-Dioxygenase: A QM/MM Study Reveals the Role of His162", Inorg. Chem., 55, 11727-11735; DOI 10.1021/acs.inorgchem.6b01732;  Unfortunately, the results in ref. 15 are incorrectly described in this article: Mutants of Arg127 were inactive in the experiments, not active.

  217. O. Caldararu, M. A. Olsson, C. Riplinger, F. Neese, U. Ryde (2017) "Binding free energies in the SAMPL5 octa-acid host–guest challenge calculated with DFT-D3 and CCSD(T)", J. Comp.-Aided Mol. Design, 31, 87-106; DOI 10.1007/s10822-016-9957-5; Open Access.

  218. E. D. Hedegård, U. Ryde (2017) "Multiscale Modelling of Lytic Polysaccharide Monooxygenases", ACS Omega, 2, 536-545; DOI 10.1021/acsomega.6b00521; Open Access.

  219. G. Dong, U. Ryde (2017) "Effect of the protein ligand in DMSO reductase studied by computational methods" J. Inorg. Biochem., 171, 45-51; DOI 10. ​1016/​j.​jinorgbio.​2017.​03.​004.

  220. G. Dong, Q. M. Phung, S. D. Hallaert, K. Pierloot, U. Ryde (2017) "H2 binding to the active site of [NiFe] hydrogenase studied by multiconfigurational and coupled-cluster methods", Phys. Chem. Chem. Phys., 19, 10590-10610; DOI 10.1039/C7CP01331K; Open Access.

  221. M. A. Olsson, U. Ryde (2017) "Comparison of methods to obtain ligand-binding free energies with QM/MM methods", J. Chem. Theory Comput., 13, 2245-2253; DOI 10.1021/acs.jctc.6b01217; Open Access.

  222. E. D. Hedegård, U. Ryde (2017) "Targeting the Reactive Intermediate in Polysaccharide Monooxygenases" J. Biol. Inorg. Chem., 22, 1029-1037, DOI 10.1007/s00775-017-1480-1; Open Access; highlighted as an article of exceptional interest in SBIC newsletter april 2019.

  223. L. Cao, O. Caldararu, U. Ryde (2017) "Protonation states of homocitrate and nearby residues in nitrogenase studied by computational methods and quantum refinement" J. Phys. Chem B, 121, 8242-8262; DOI 10.1021/acs.jpcb.7b02714; free reprints.

  224. U. Ryde (2017) "How many conformations need to be sampled to obtain converged QM/MM energies? The curse of exponential averaging" J. Chem. Theory Comput. 13, 5745-5752; DOI 10.1021/acs.jctc.7b00826; free reprints.

  225. F. Manzoni, J. Uranga, S. Genheden, U. Ryde (2017) Can system truncation speed up ligand-binding calculations with periodic free-energy simulations? J. Chem. Inf. Model., 57, 2865-2873; DOI 10.1021/acs.jcim.7b00324; free reprints.

  226. F. Sadat Alavi, M. Zahedi, N. Safari, U. Ryde (2017) "QM/MM study of the conversion of oxophlorin into verdoheme by heme oxygenase", J. Phys. Chem. B 121, 11427-11436; DOI 10.1021/acs.jpcb.7b08332; free reprints.

  227. L. Cao, O. Caldararu, A. C. Rosenzweig, U. Ryde (2018) "Quantum refinement does not support dinuclear copper sites in crystal structures of particulate methane monooxygenase", Angew. Chem. Int. Ed., 57, 162-166; DOI 10.1002/anie.201708977; Recommended by F1000.

  228. M. A. Olsson, A. T. García-Sosa, U. Ryde (2018) "Binding affinities of the farnesoid X receptor in the D3R Grand Challenge 2 estimated by free-energy perturbation and docking" J. Comput.-Aided Mol. Des., 32, 211-224; DOI 10.1007/s10822-017-0056-z; Open Access.

  229. G. Dong, U. Ryde, H. J. Aa. Jensen, E. D. Hedegård (2018) "Exploration of H2 binding to the [NiFe]-hydrogenase active site with multiconfigurational density functional theory", Phys. Chem. Chem. Phys., 20, 794-801; DOI 10.1039/C7CP06767d; Open Access. Part of the collection PCCP 2018 hot articles.

  230. M. Misini Ignjatovi ć, P. Mikulskis, P. Söderhjelm, U. Ryde (2018) "Can MM/GBSA calculation be sped up by system truncation?" J. Comput. Chem., 39, 361-372; DOI 10.1002/jcc.25120.

  231. G. Dong, L. Cao, U. Ryde (2018) "Insight into the reaction mechanism of lipoyl synthase: A QM/MM study, J. Biol. Inorg. Chem, 23, 221-229; DOI 10.1007/s00775-017-1522-8; Open Access.

  232. O. Caldararu, M. Feldt, D. Cioloboc, M.-C. van Severen, K. Starke, R. A. Mata, E. Nordlander, U. Ryde (2018) "QM/MM study of the reaction mechanism of sulfite oxidase", Sci. Rep. 8, 4684; DOI 10.1038/s41598-018-22751-6; Open Access.

  233. L. Cao & U. Ryde (2018) "On the difference between additive and subtractive QM/MM calculations", Front. Chem., 6, 89; DOI 10.3389/fchem.2018.00089; Open Access.

  234. F. Manzoni, U. Ryde (2018) "Assessing the stability of free-energy perturbation calculations by performing variations in the method" J. Comput.-Aided Mol. Des., 32, 529-536; DOI 10.1007/s10822-018-0110-5; Open Access.

  235. E. D. Hedegård, U. Ryde (2018) "Molecular mechanism of lytic polysaccharide monooxygenases", Chem. Sci., 9, 3866-3880; DOI 10.1039/c8sc00426a; Open Access.

  236. S. Jafari, N. Kazemi, U. Ryde, M. Irani (2018) "Higher flexibility of Glu-172 explains the unusual sterospecificity of glyoxalase I", Inorg. Chem., 57, 4944-4958; DOI 10.1021/acs.inorgchem.7b03215.

  237. C. Steinmann, M. A. Olsson & U. Ryde (2018) "Relative ligand-binding free energies calculated from multiple short QM/MM MD simulations", J. Chem. Theory Comput., 14, 3228-3237; DOI 10.1021/acs.jctc.8b00081.

  238. F. S. Alavi, M. Gheidi, M. Zahedi, N. Safari, U. Ryde (2018) "A novel mechanism of heme degradation to biliverdin studied by QM/MM and QM calculations", Dalton Trans., 47, 8283-8291; DOI 10.1039/c8dt00064f.

  239. L. Cao & U. Ryde (2018) "Influence of the protein and DFT method on the broken-symmetry and spin states in nitrogenase", Int. J. Quant. Chem., 118, e25627; DOI 10.1002/qua.25627.

  240. A. Genoni, L. Bucinsky, N. Claiser, J. Contreras-Garcia, B. Dittrich, P. M. Dominiak, E. Espinosa, C. Gatti, P. Giannozzi, J.-M. Gillet, D. Jayatilaka, P. Macchi, A. Ø. Madsen, L. J. Massa, C. F. Matta, K. M. Merz, P. N. H. Nakashima, H. Ott, U. Ryde, K. Schwarz, M. Sierka, S. Grabowsky (2018) "Quantum Crystallography: Current Developments and Future Perspectives", Chem. Eur. J., 24, 10881-10905; DOI 10.1002/chem.201705952; Review article.

  241. G. Dong & U Ryde (2018) "Reaction mechanism of formate dehydrogenase studied by computational methods" J. Biol. Inorg. Chem., 23, 1243-1254; DOI 10.1007/s00775-018-1608-y; Open Access.

  242. O. Caldararu, M. A. Olsson, M. Misini Ignjatović, M. Wang, U. Ryde (2018) "Binding free energies in the SAMPL6 octa-acid host-guest challenge calculated with MM and QM methods" J. Comput.-Aided Mol. Design, 32, 1027-1046; DOI 10.1007/s10822-0158-2; Open Access.

  243. L. Cao, O. Caldararu, U. Ryde (2018) "Protonation and reduction of the FeMo cluster in nitrogenase studied by quantum mechanics/molecular mechanics (QM/MM) calculations", J. Chem. Theory Comput., 14, 6653–6678; DOI 10.1021/acs.jctc.8b00778.

  244. M. Wang, Y. Mei & U. Ryde (2018) "Predicting relative binding affinity using nonequilibrium QM/MM simulations", J. Chem. Theory Comput., 14, 6613-6622; DOI 10.1021/acs.jctc.8b00685.

  245. G. Dong, Q. M. Phung, K. Pierloot & U. Ryde (2018) "Reaction mechanism of [NiFe] hydrogenase studied by computational methods", Inorg. Chem., 57, 15289-15298; DOI 10.1021/acs.inorgchem.8b02590.

  246. O. Caldararu, E. Oksanen, U. Ryde, E. D. Hedegård (2019) "Mechanism of hydrogen peroxide formation by lytic polysaccharide monooxygenase", Chem. Sci., 10, 576-586; DOI 10.1039/C8SC03980A; Correction: Chem. Sci., 10 (2019) 8262-8263; DOI 10.1039/C9SC90191D; Open Access.

  247. L. Cao & U. Ryde (2019) "Extremely large differences in DFT energies for nitrogenase models", Phys. Chem. Chem. Phys., 21, 2480-2488; DOI 10.1039/C8CP06930A; Open Access.

  248. R. Kumar, K. Peterson, M. Misini Ignjatović, H. Leffler, U. Ryde, U. J. Nilsson, D. T. Logan (2019) "Substituted polyfluoroaryl interactions with an arginine side chain in galectin-3 are governed by steric-, desolvation and electronic conjugation effects" Org. Biomol. Chem., 17, 1081-1089; DOI 10.1039/C8OB02888E; Open Access.

  249. M. L. Verteramo, O. Stenström, M. Misini Ignjatović, O. Caldararu, M. A. Olsson, F. Manzoni, H. Leffler, E. Oksanen, D. Logan, U. Nilsson, U. Ryde, M. Akke, (2019) "Interplay between conformational entropy and solvation entropy in protein–ligand binding", J. Am. Chem. Soc., 141, 2012-2026; DOI 10.1021/jacs.8b11099; Open Access.

  250. A. Rovaletti, M. Bruschi, G. Moro, U. Cosentino, U. Ryde, C. Greco (2019) "A thiocarbonate sink on the enzymatic energy landscape of aerobic CO oxidation? Answers from DFT and QM/MM models of Mo-Cu CO-dehydrogenases", J. Catal., 372, 201-205; DOI 10.1016/j.jcat.2019.02.032.

  251. O. Caldararu, F. Manzoni, E. Oksanen, D. T. Logan & U. Ryde (2019) "Refinement of protein structures using a combination of quantum mechanical calculations with neutron and X-ray crystallographic data" Acta Cryst. D, 75, 368-380; DOI 10.1107/S205979831900175X; Open Access.
    Correction    : Acta Cryst. D, 76 (2020) 85-86; DOI 10.1107/S2059798319016383.

  252. M. Wang, Y. Mei, U. Ryde (2019) "Host-Guest relative binding affinities at density-functional theory level from semiempirical molecular dynamics simulations" J. Chem. Theory Comput. 15, 2659-2671; DOI 10.1021/acs.jctc.8b01280.

  253. F. S. Alavi, N. Safari, U. Ryde, M. Zahedi (2019) "QM/MM study of the conversion of biliverdin into verdoheme by heme oxygenase", Theor. Chem. Acc., 138, 72 (8 pages); DOI 10.1007/s00214-019-2461-y.

  254. L. Cao, M. C. Börner, J. Bergmann, O. Caldararu & U. Ryde (2019) "Geometry and electronic structure of the P-cluster in nitrogenase studied by QM/MM and quantum refinement", Inorg. Chem., 58, 9672-9690; DOI 10.1021/acs.inorgchem.9b00400;  selected for ACS Editors' Choice; Open Access.

  255. R. Kumar, M. Misini Ignjatović, K. Peterson, M. A. Olsson, H. Leffler, U. Ryde, U. J. Nilsson & D. T. Logan (2019) "Structure and energetics of ligand–fluorine interactions with galectin-3 backbone and side-chain amides – insight into solvation effects and multipolar interactions", Chem. Med. Chem., 14, 1528-1536; DOI 10.1002/cmdc.201900293; Open Access.

  256. O. Caldararu, R. Kumar, E. Oksanen, D. T. Logan & U. Ryde (2019) Are crystallographic B-factors suitable for calculating protein conformational entropy? Phys. Chem. Chem. Phys., 21, 18149-18160; DOI 10.1039/C9CP02504A; Open Access.

  257. A. Rovaletti, M. Bruschi, G: Moro, U. Cosentino, C. Greco, U. Ryde (2019) "Theoretical Insights into the Aerobic Hydrogenase Activity of Molybdenum-Copper CO Dehydrogenase", Inorganics, 7, 135; DOI 10.10390/inorganics7110135; Open Access.

  258. A. Brânzanic, U. Ryde, R. Silaghi-Dumitrescu (2019) "Importance of the iron–sulfur component and of the siroheme modification in the resting state of sulfite reductase", J. Inorg. Biochem., 203, 110928; DOI 10.1016/j.jinorgbio.2019.110928; preprint.

  259. A. Brânzanic, U. Ryde, R. Silaghi-Dumitrescu (2020) "Why does Sulfite Reductase employ Siroheme?", Chem. Commun., 55, 14047-14049; DOI 10.1039/C9CC05271B.

  260. S. Jafari, U. Ryde, M. Irani (2020) "QM/MM study of the stereospecific proton exchange of glutathiohydroxyacetone by glyoxalase I", Results Chem., 1, 100011 (12 pages); DOI 10.1039/C9CC05271B.

  261. S. Jafari, U. Ryde, G. Dong, A. Fouda, F. Sadat Alavi, M. Irani (2020) "Quantum mechanics/molecular mechanics study of the reaction mechanism of glyoxalase I", Inorg. Chem., 59, 2594-2603; DOI 10.1021/acs.inorgchem.9b03621.

  262. E. D. Larsson, G. Dong, V. Veryazov, U. Ryde, E. Hedegård (2020), "Is density functional theory accurate for lytic polysaccharide monooxygenase enzymes?" Dalton Trans., 49, 1501-1512; DOI 10.1039/c9dt04486h; Open Access.

  263. M. Hedrén, M. Zhou, M. Montes, & U. Ryde (2020) "Rubus wendtii, a new blackberry species from Scania, southern Sweden", Svensk Bot. Tidskr, 114, 22-31; Rubus.

  264. O. Caldararu, M. Misini Ignjatović, E. Oksanen & U. Ryde (2020) "Water structure in solution and crystal molecular dynamics simulations compared to protein crystal structures", RSC Advances, 10, 8435-8443; DOI 10.1039/c9ra09601a; Open Access.

  265. J. Bergmann, M. Davidson, E. Oksanen, U. Ryde and D. Jayatilaka (2020) "fragHAR: towards ab initio quantum crystallographic X-ray structure refinement for polypeptides and proteins", IUCrJ, 7, 158-165; DOI 10.1107/S2052252519015975; Open Access.

  266. L. Cao & U. Ryde (2020) "What is the structure of the E4 intermediate in nitrogenase?", J. Chem. Theory Comput., 16, 1936-1952; DOI 10.1021/acs.jctc.9b01254; Open Access.

  267. L. Cao & U. Ryde (2020) "N2H2 binding to the nitrogenase FeMo cluster studied by QM/MM methods" J. Biol. Inorg. Chem., 25, 521-540; DOI 10.1007/s00775-020-01780-5; Open Access.

  268. L. Cao & U. Ryde (2020) "Putative reaction mechanism of nitrogenase after dissociation of a sulfide ligand", J. Catal., 391, 247-259; DOI 10.1016/j.jcat.2020.08.028; Open Access.

  269. L. Cao, O. Caldararu & U. Ryde (2020) "Does the crystal structure of vanadium nitrogenase contain a reaction intermediate? Evidence from quantum refinement" J. Biol. Inorg. Chem., 25, 847-861; DOI 10.1007/s00775-020-01813-z; Open Access.

  270. A. Eriksson, O. Caldararu, U. Ryde and E. Oksanen (2020) "Automated Orientation of Water Molecules in Neutron Structures of Proteins", Acta Crystal. D, 76, 1025-1032; DOI 10.1107/S2059798320011729.

  271. L. Cao & U. Ryde (2020) "Quantum refinement with multiple conformations; applications to the P-cluster in nitrogenase", Acta Crystal. D, 76, 1145-1156; DOI 10.1107/S2059798320012917; Open Access.

  272. S. Jafari, U. Ryde, M. Irani (2021) "Two-substrate glyoxalase I mechanism; a quantum mechanics/molecular mechanics study", Inorg. Chem., 60, 303-314; DOI 10.1021/acs.inorgchem.0c02957.

  273. A. Rovaletti, C. Greco & U. Ryde (2021) "QM/MM study of the binding of H2 to MoCu CO dehydrogenase: Development and applications of improved H2 van der Waals parameters" J. Mol. Model., 27, 68; DOI 10.1007/s00894-020-04655-3; Open Access.

  274. S. Jafari, U. Ryde, M. Irani (2021) "QM/MM study of the Catalytic Reaction of Myrosinase; Importance of Assigning Proper Protonation States of Active-site Residues", J. Chem. Theory Comput, 17, 1822-1841; DOI 10.1021/acs.jctc.0c01121; Open Access.

  275. J. Bergmann, E. Oksanen, U. Ryde (2021) "Quantum-refinement studies of the bidentate ligand of V-nitrogenase and the protonation state of CO-inhibited Mo-nitrogenase", J. Inorg. Biochem. 219, 111426; DOI: 10.1016/j.jinorgbio.2021.111426; Open Access.

  276. J. Bergmann, E. Oksanen & U. Ryde (2021) "Critical evaluation of a crystal structure of nitrogenase with bound N2 ligands", J. Biol. Inorg. Chem., 26, 341-353; DOI 10.1007/s00775-021-01858-8; Open Access.

  277. J. Wallerstein, V. Ekberg, M. Misini Ignjatović, R. Kumar,  O. Caldararu, K. Peterson,  S. Wernersson, U. Brath, H. Leffler, E. Oksanen, D. Logan, U. Nilsson, U. Ryde, M. Akke (2021) "Entropy–entropy compensation between the protein, ligand, and solvent degrees of freedom fine-tunes affinity in ligand binding to galectin-3C", J. Am. Chem. Soc. Au, 1, 484-500; DOI: 10.1021/jacsau.0c00094; Open Access.

  278. V. Kelpsas, O. Caldararu, M. P. Blakeley, N. Coquelle, R. K. Wierenga, U. Ryde, C. von Wachenfeldt, E. Oksanen (2021) "Neutron structures of Leishmania mexicana triosephosphate isomer-ase complexes with reaction intermediate mimics shed light on the proton shuttling steps", Int. Uni. Cryst. J., 8, 633-643; DOI: 10.1107/S2052252521004619.; Commentary: https://doi.org/10.1107/S205225252100573X; Open Access.

  279. O. Caldararu, V. Ekberg, D. T. Logan, E. Oksanen and U. Ryde (2021) "Exploring ligand dynamics in protein crystal structures with ensemble refinement", Acta Cryst. D, 77, 1099-1115; DOI 10.1107/S2059798321006513; Open Access; recommended in Faculty Opinions.

  280. J. Bergmann, E. Oksanen, U. Ryde (2022) "Combining crystallography with quantum mechanics", Curr. Opin. Struct. Biol., 72 18-26; DOI: 10.1016/j.sbi.2021.07.002; Review article; Open Access.

  281. V. Ekberg, U. Ryde (2021) "On the use of interaction entropy and related methods to estimate binding entropies", J. Chem. Theory Comput., 17, 5379-5391; DOI: 10.1021/acs.jctc.1c00374; Open Access.

  282. K. A. Lye & U. Ryde (2021) Norske bjørnebær 6. Sørlandsbjørnebær Rubus "firmus", Blyttia, 79, 39-45; Rubus.

  283. M. Torbjörnsson, U. Ryde (2021) "Comparison of the accuracy of DFT methods for  reactions with relevance to nitrogenase", Electron. Struct., 3, 034005; DOI: 10.1088/2516-1075/ac1a63; Open Access.

  284. U. Ryde, M. S. Montes,  M. Zhou, T. Mattsson, T. Burén, M. Hedrén,  (2021) "Hybrids between Rubus idaeus and Rubus Sect. Corylifolii and their relation to R. pruinosus and R. rosanthus" Nordic J. Bot., 39:e03111; DOI: 10.1111/njb.03111. Raw data in Dryad: https://doi.org/10.5061/dryad.3j9kd51j3; Open Access; Rubus.

  285. J. Bergmann, E. Oksanen, U. Ryde (2021) "Can the results of quantum refinement be improved with a continuum-solvation model?” Acta Cryst. B, 77, 906-918; DOI 10.1107/S2052520621009574; Open Access.

  286. H. Jiang, U. Ryde (2022) "Thermodynamically favourable states in the reaction of nitrogenase without dissociation of any sulfide ligand", Chem. Eur. J., 28, e202103933; DOI 10.1002/chem.202103933; Open Access.

  287.  A. Rovaletti, G. Moro, U. R. Cosentino, U. Ryde, C Greco (2022) "Can water act as a nucleophile in CO oxidation catalysed by Mo/Cu CO-dehydrogenase? Answers from theory", Chem. Phys. Chem., 23, e202200053; DOI 10.1002/cphc.202200053; Open Access.

  288. S. Jafari, Y. A. Tavares Santos, J. Bergmann, M. Irani, U. Ryde (2022) "Benchmark study of redox potentials calculation for iron–sulfur clusters in proteins”, Inorg. Chem., 61, 5991-6007; DOI: 10.1021/acs.inorgchem.1c03422; Open Access.

  289. D. Cirri, C. Bazzicalupi, U. Ryde, J. Bergmann, F. Binacchi, A. Nocentini, A. Pratesi, P. Gratteri, L. Messori (2022) "Computationally enhanced X-ray diffraction analysis of a gold(III) complex interacting with the human telomeric DNA G-quadruplex. Unravelling non-unique ligand positioning", Int. J. Biol. Macromol., 211, 506-513; DOI: 10.1016/j.ijbiomac.2022.05.033.

  290. V. Ekberg, M. L. Samways, M. Misini Ignjatović, J. W. Essex  & U. Ryde (2022) "Comparison of Grand Canonical and Conventional Molecular Dynamics Simulation Methods for Protein-Bound Water Networks", ACS J. Phys. Chem. Au, 2, 247-259; DOI: 10.1021/acsphyschemau.1c00052; Open Access.

  291. A. Ritacca, A. Rovaletti, G. Moro, U. Cosentino, U. Ryde, E. Sicilia, C. Greco (2022) "Unravelling the reaction mechanism of Mo/Cu CO dehydrogenase using QM/MM calculations", ACS Catalysis, 12,7336-7343; DOI: 10.1021/acscatal.2c01408; Open Access.

  292. H. Jiang, O. K. G. Svensson, L. Cao & U. Ryde (2022) "Proton transfer pathways in nitrogenase with and without dissociated S2B" Angew. Chemie, 61, e202208544 (9 pages); DOI: 10.1002/anie.202208544; Open Access. Among the most popular articles Nov. 2022.

  293. H. Jiang, O. K. G. Svensson & U. Ryde (2022) "QM/MM study of partial dissociation of S2B for the E2 intermediate of nitrogenase" Inorg. Chem., 61, 18067-18076; DOI: 10.1021/acs.inorgchem.2c02488; Open Access.

  294. M. Lewin, M. S. Montes, M. Zhou, T. Mattsson, T. Burén, M. Hedrén & U. Ryde (2022) "Hybrids between Rubus caesius and Rubus Sect. Corylifolii and their relation to R. cyclomorphus, R. tiliaster, R. glauciformis, R. slesvicensis and R. firmus" Nordic J. Bot., 2022, e033759, 18 pages; DOI: 10.1111/njb.03759. Open Access; Rubus; Raw data in Dryad: https://doi.org/10.5061/dryad.6q573n62f.

  295. A. Rovaletti, U. Ryde, G. Moro, U. Cosentino, C. Greco (2022) "How general is the effect of the bulkiness of organic ligands on the basicity of metalorganic catalysts? H2-evolving Mo oxides/sulphides as case studies", Phys. Chem. Chem. Phys., 24,29471-29479, DOI: 10.1039/D2CP03996F; Open Access.

  296. H. Jiang, O. K. G. Svensson & U. Ryde (2023) "Quantum mechanical calculations of redox potentials of the metal clusters in nitrogenase", Molecules 28, 65; DOI: 10.3390/molecules28010065; Open Access.

  297. M. Torbjörnsson, M. M. Hagemann, U. Ryde & E. D. Hedegård (2023) "Histidine oxidation in lytic polysaccharide monooxygenase", J. Biol. Inorg. Chem., 28, 317-328; DOI 10.1007/s00775-023-01993-4; Open Access.

  298. W. Meelua, T. Wanjai, N. Thinkumrob, J. Oláh, J. R. Ketudat-Cairns, S. Hannongbua, U. Ryde & J. Jitonnom (2023) "Computational study of the reaction mechanism and stereospecificity of dihydropyrimidinase" Phys. Chem. Chem. Phys., 25, 8767-8778; DOI 10.1039/d2cp05262h.

  299. J. Shirazi, S. Jafari, U. Ryde, M. Irani (2023) "Catalytic reaction mechanism of Glyoxalase II, a quantum mechanics/molecular mechanics study", J. Phys. Chem. B., 127, 4480-4495; DOI 10.1021/acs.jpcb.3c01495.

  300. S. Scrima, M. Tiberti, U. Ryde, M. Lambrughi, E. Papaleo (2023) "Comparison of force fields to study the zinc-finger containing protein NPL4, a target for disulfiram in cancer therapy", Biochem. Biophys. Acta, Prot. Proteom., 140921; DOI 10.1016/j.bbapap.2023.140921.

  301. H. Jiang & U. Ryde (2023) "N2 binding to the E0–E4 states of nitrogenase", Dalton Transactions, 52, 9104-9120; DOI 10.1039/d3dt00648d; Open Access.

  302. S. Jafari, M. Irani & U. Ryde (2023) "Two local minima for structures of [4Fe– 4S] clusters obtained with density functional theory methods", Sci. Rep., 13, 10832; DOI 10.1038/s41598-023-37755-0; Open Access.

  303. V. Vysotskiy, M. Torbjörnsson, H. Jiang, E. D. Larsson, L. Cao, U. Ryde, H. Zhai, S. Lee, G. K.-L. Chan (2023) "Assessment of DFT functionals for a minimal nitrogenase [Fe(SH)4H]– model employing state-of-the-art ab initio methods", J. Chem. Phys, 159, 044106; DOI: 10.1063/5.0152611; Open Access.

  304. H. Jiang, K. J. M. Lundgren & U. Ryde (2023) "Protonation of homocitrate and the E1 state of Fe-nitrogenase studied by QM/MM calculations", Inorg. Chem., 62, 19433-19445 ; DOI: 10.1021/acs.inorgchem.3c02329; Open Access.

  305. H. Zhai, S. Lee, Z.-H. Cui, L. Cao, U. Ryde, G. K.-L. Chan (2023) "Multireference protonation energetics of a dimeric model of nitrogenase iron-sulfur clusters", J. Phys. Chem. A, 127, 9974-9984; DOI: 10.1021/acs.jpca.3c06142; Open Access.

  306. A. van de Beek, D. Drenckhahn, H. DeVriese, T. Gregor, E. van den Ham, R. Haveman, M. Hohla, G. Kiraly, P. Kosiński, G. Matzke-Hajek, K. Meijer, D. P. Mercier, I. de Ronde, U. Ryde & B. Travnicek (2023) "Proposal to reject the name Rubus pseudoidaeus (Rosaceae)" Taxon, 72, 673-674; DOI: 10.1002/tax.12971; Rubus; Open Access.

  307. H. Jiang & U. Ryde (2024) "H2 formation from the E2–E4 states of nitrogenase", PhysChemChemPhys, 26, 1364–1375; DOI 10.1039/D3CP05181A; Open Access.

  308. V. Vysotskiy, C. Filippi, U. Ryde (2024) "Scalar relativistic all-electron and pseudopotential ab initio study of a minimal nitrogenase [Fe(SH)4H]– model  employing coupled-cluster and auxiliary-field quantum Monte Carlo many-body methods", J. Phys. Chem. A, 128, 1358–1374; DOI: 10.1021/acs.jpca.3c05808; Open Access.

  309. S. Jafari, U. Ryde, M. Irani, (2024) "QM/MM study of the catalytic reaction of aphid myrosinase", Int. J. Biol. Macromol., 262, 130089 ; DOI: 10.1016/j.ijbiomac.2024.130089; free copies.

  310. M. L. Verteramo, M. M. Ignjatović, R. Kumar, S. Wernersson, V. Ekberg, J. Wallerstein, G. Carlström, V. Chadimová, H. Leffler, F. Zetterberg, D. T. Logan, U. Ryde, M. Akke & U. J. Nilsson (2024) "Interplay of halogen bonding an and solvation in protein–ligand binding", iScience, 27, 109636; DOI: 10.1016/j.isci.2024.109636; Open Access.

  311. A. Rovaletti, M. Giorgio, U. Cosentino, U. Ryde & C. Greco (2024) "CO oxidation mechanism of silver-substituted Mo/Cu CO-dehydrogenase. Analogies and differences to the native enzyme", ChemPhysChem; DOI: 10.1002/cphc.202400293; Open Access.

  312. M. Wang, Y. Mei & U. Ryde (2024) "Convergence criteria for single-step free-energy calculations: The relation between the π bias measure and the sample variance" Chem. Sci, 15, 8786-8799; DOI: 10.1039/D4SC00140K; Open Access.

  313. M. Wang, B. Fan, W. Lu, Y. Chang, D. Han, J. Lu, T. Liu, Q. Gao, C. Chen, U. Ryde & Y. Xu (2024) "Molecular Dynamics Simulations Reveals Binding Mechanisms of Cyclic Dinucleotides with Human STING Protein", Molecules., 29, 2650; DOI: 10.3390/molecules.29112650; Open Access.

  314. M. Zhou, M. S. Montes, T. Mattsson, T. Burén, M. Hedrén & U. Ryde (2024) "Rubus wahlbergii and related species in Sweden" Nordic J. Bot., submitted 8/1-24; revised version submitted 11/3; second revised version submitted 2/5; 3rd revised version submitted 20/5; accepted 22/5; Nordic J. Bot., 2022, e033759, 18 pages; DOI: 10.1111/njb.04373. Open Access; Rubus; Raw data in Dryad, DOI: 10.5061/dryad.3bk3j9ktf.

  315. J. Shirazi, S. Jafari, U. Ryde, M. Irani, (2024) "Metal Preference of Glyoxalase II, a Quantum Mechanics/Molecular Mechanics Study", Inorg. Chem., submitted 21/1-24.

  316. I. Bolaño Losada, U. Ryde, P. Persson (2024) "Understanding anomalous cage-escape dynamics in photoredox processes driven by Fe(III) N-heterocyclic carbene complexes", J. Am. Chem. Soc., submitted 14/2-24.

  317. K. J. M. Lundgren, O. Caldararu, E. Oksanen & Ulf Ryde (2024) "Quantum refinement in real and reciprocal space", IUCrJ, submitted 27/2-24.

  318. H. Jiang & U. Ryde (2024) "Putative reaction mechanism of nitrogenase with a half-dissociated S2B ligand", Dalton Trans., submitted 29/3-24; revised version submitted 22/5.

  319. H. Jiang & U. Ryde (2024) "Reaction mechanism for CO reduction by Mo-nitrogenase studied by QM/MM", ACS Catal., submitted 11/4-24; transferred to Inorg. Chem. Revision submitted 5/6.

22 of the publications are not original articles: 14 (Ph.D. thesis), 28, 39, 49, 63, 103, 127, 170, 212 (book chapters), 51, 58, 60, 81, 94, 135, 176, 180, 189, 204, 209, 240, 280 (review articles); 7 of the publications are in botany (Rubus): 132, 137, 146, 166, 263, 282, 284.

19 247 citations in Google Scholar, October 2022; h index 74; i10 230.

List of publications in LUCRIS; here at least preprints are available for almost all publications