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.
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.
G. Pettersson,
U. Ryde-Pettersson (1988) "A mathematical model of the Calvin
photosynthesis cycle" Eur. J. Biochem. 175, 661-672.
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.
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.
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.
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.
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.
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.
U. Ryde-Pettersson (1990) "On the mechanistic origin of damped oscillations in biochemical reaction system". Eur. J. Biochem. 194, 431-436.
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.
U. Ryde-Pettersson (1992) "Oscillations in coupled enzymic reactions at high concentration of enzyme". Biochim. Biophys. Acta 1119 , 118-122
U. Ryde-Pettersson (1992) "Oscillations in the photosynthetic Calvin cycle - examination of a mathematical model". Acta Chem. Scand. 46, 406-408.
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.
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. Abstract
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. Abstract
U. Ryde (1995) "On the role of Glu68 in alcohol dehydrogenase", Protein Science 4, 1124-1132. Abstract
L. Hemmingsen, U. Ryde (1996) "Ab initio calculations of electric field gradients in cadmium complexes". J. Phys. Chem. 100 , 4803-4809. Abstract
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. Abstract
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. Abstract
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
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. Abstract
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. Link
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. Link
E. Sigfridsson, U. Ryde (1998) "A 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
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. Abstract
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. Abstract
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. Abstract
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.
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
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. Link
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.
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.
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.
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.
U. Ryde (1999) "Carboxylate binding modes in zinc proteins, a theoretical study". Biophys. J. 77, 2777-2787.
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.
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
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.
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
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
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
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 .
M. H. M. Olsson, U. Ryde (2001) "Geometry, reduction potential, and reorganisation energy of the binuclear Cu A site, studied by theoretical methods", J. Am. Chem. Soc., 123, 7866-7876. Free reprint DOI 10.1021/ja010315u
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
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
U. Ryde, L. Olsen, K. Nilsson (2002) "Quantum chemical geometry optimisations in proteins using crystallographic raw data", J. Comp. Chem., 23, 1058-1070. DOI 10.1002/jcc.10093 .
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.
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.
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.
U. Ryde (2003) "Combined quantum and molecular mechanics calculations on metalloproteins", Curr. Opin. Chem. Biol., 7, 136-142.
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
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.
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.
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 .
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.
K. P. Jensen, U. Ryde (2003) "Importance of proximal hydrogen bonds in haem proteins", Mol. Phys., 101, 2003-2018.
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 .
K. P. Jensen, U. Ryde (2003) "Theoretical prediction of the Co-C bond strength in cobalamins", J. Phys. Chem. B, 107, 7539-7545; DOI: 10.1021/jp027566p; Free reprint.
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.
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.
U. Ryde, K. Nilsson (2003) "Quantum chemistry can improve protein crystal structures locally", J. Am. Chem. Soc., 125, 14232-14233; DOI: 10.1021/ja0365328; free reprint.
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.
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.
K. P. Jensen, U. Ryde (2004) "How O2 binds to heme: Reasons for rapid binding and spin inversion", J. Biol. Chem., 279, 14561-14569.
Y. Shen, U. Ryde (2004) "The structure of sitting-atop complexes of metalloporphyrins studied by theoretical methods", J. Inorg. Biochem., 98, 878-895.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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
T. H. Rod, U. Ryde (2005) "Free energy barriers at the density functional theory level: methyl transfer catalyzed by catechol O-methyltransferase", J. Chem. Theory Comput., 1, 1240-1251; DOI: 10.1021/ct0501102.
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.
Y.-W. Hsiao, U. Ryde (2005) "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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
J. Chalupský, F. Neese, E. I. Solomon,U. Ryde, L. Rulíšek (2006) "Identification of intermediates in the reaction cycle of multicopper oxidases by quantum chemical calculations of spectroscopic parameters", Inorg. Chem., 45, 11051-11059; DOI: 10.1021/ic0619512; free reprints.
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.
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.
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.
U. Ryde, Y.-W. Hsiao, L. Rulíšek, E. I. Solomon (2007) "Identification of the peroxy adduct in multi-copper oxidases by a combination of computational chemistry and EXAFS measurements", J. Am. Chem. Soc., 129, 726-727; DOI: 10.1021/ja062594g; free reprints.
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.
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.
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.
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.
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).
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
P. Rydberg, U. Ryde, L. Olsen (2008) "Prediction of activation energies for aromatic oxidation by cytochrome P450", J. Phys. Chem. A, 2008, 112, 13058-13063; DOI: 10.1021/jp803854v.
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.
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.
K P. Jensen, U. Ryde (2009) "Cobalamins uncovered by
modern electronic structure calculations", Coord. Chem. Rev., 253.
769-778.
P. Söderhjelm, U. Ryde (2009) "Conformational dependence of charges in protein simulations", J. Comput. Chem., 30, 750-760; DOI: 10.1002/jcc.21097.
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.
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.
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
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
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.
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.
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.
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.
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.
G. Zoppellaro, K. L. Bren, A. A. Ensign, E. Harbitz, R. Kaur, H.-P. Hersleth, U. Ryde, L. Hederstedt, K. K. Andersson, "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.
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.
U. Ryde (2009) "Rubus sect. Corylifolii in the province of Halland, SW Sweden", Svensk Bot. Tidskr. 103, 279-300.
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.
S. Genheden, U.
Ryde (2010) "How to obtain statistically
converged MM/GBSA results", J. Comput. Chem., 31, 837-846; DOI: 10.1002/jcc.21366.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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); chosen for JACS select.
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
U. Ryde, G.
Werlemark (2010) "Rubus sordirosanthus in Halland, southwest
Sweden", Svensk Bot. Tidskr. 104, 405-413.
S. Genheden, U. Ryde "A comparison of different initialisation protocols to obtain statistically independent molecular dynamics simulations" J. Comput. Chem. 2011, 32, 187-195; DOI 10.1002/jcc.21564.
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.
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.
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.
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.
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.
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.
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.
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.
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.
S. Genheden, P. Mikulskis, L. Hu, J. Kongsted, P. Söderhjelm, U. Ryde "Accurate predictions of non-polar solvation free energies require explicit consideration of binding site hydration", J. Am. Chem. Soc., 2011, 133, 13081-13092; DOI 10.1021/ja202972m.
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.
C. Greco, L. De Gioia, U. Ryde "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.
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.
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.
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.
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.
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.
J. Heimdal, M. Kaukonen, M. Srnec, L. Rulíšek, U. Ryde "Reduction potentials and acidity constants of Mn 5superoxide dismutase calculated by QM/MM free-energy methods" Chem. Phys. Chem., 2011, 12, 3337-3347; DOI 10.1002/cphc.201100339.
U. Ryde "in" Nordic J. Bot., 2011, 29, 708-721; DOI 10,1111/j.1756-1051.2011.01203.x.
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).