Source: http://signe.teokem.lu.se/~ulf/references.html
Timestamp: 2019-04-24 08:00:59+00:00

Document:
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.
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.
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.
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.
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.
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.
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.
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.
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; DOI: 10.1111/j.1432-1033.1990.tb15636.x; Open access.
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.
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.
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. .
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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 .
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.
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. Book Chapter.
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.
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.
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; DOI 10.1080/0026897031000109383.
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.
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.
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.
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 locally improve protein crystal structures ", 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. Book Chapter.
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; DOI: 10.1074/jbc.M314007200; Open access.
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.
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.
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.
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.
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.
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.
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) "Multireference ab initio calculations on reaction intermediates of multicopper oxidases", 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. Review article.
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 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.
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. Book Chapter.
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; DOI: 10.1002/cbdv.200890189.
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, 13058-13065; 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) "Conformational dependence of charges in protein simulations", J. Comput. Chem., 30, 750-760; DOI: 10.1002/jcc.21097.
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.
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. Book Chapter.
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 (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.
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; pdf.
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. Review article.
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.
culations", 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; pdf; chosen for JACS select.
U. Ryde, G. Werlemark (2010) "Rubus sordirosanthus in Halland, southwest Sweden", Svensk Bot. Tidskr. 104, 405-413; pdf.
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.
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 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.
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, 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.
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 superoxide dismutase calculated by QM/MM free-energy methods" Chem. Phys. Chem., 2011, 12, 3337-3347; DOI 10.1002/cphc.201100339.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Genheden, S.; Kuhn, O.; Mikulskis, P.; Hoffmann, D.; Ryde, U. "The normal-mode enetropy 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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
U. Ryde (2014) "A fundamental view of enthalpy–entropy compensation" Med. Chem. Commun., 5, 1324-1336; DOI: 10.1039/C4MD00057A; Open access; pdf.
M.-C. van Severen, M. Andrejic, 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.
M. Andrejic, 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.
P. Mikulskis, S. Genheden, U. Ryde (2014) "A large-scale test of free-energy simulation estimates of protein-ligand binding affinities", J. Chem. Inf. Model., 54, 2794-2806; DOI: 10.1021/ci5004027; Open Access; pdf.
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.
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.
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.
E. D. Hedegård, U. Ryde (2017) "Multiscale Modelling of Lytic Polysaccharide Monooxygenases", ACS Omega, 2, 536-545; DOI 10.1021/acsomega.6b00521; Open Access.
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.
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.
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.
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.
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.
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.
F. S. 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.
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.
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.
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.
M. Misini Ignjatović, 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.
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.
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.
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.
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.
E. D. Hedegård, U. Ryde (2018) "Molecular mechanism of lytic polysaccharide monooxygenases", Chem. Sci., 9, 3866-3880; DOI 10.1039/c8sc00426a; Open Access.
S. Jafari, N. Kazemi, U. Ryde, M. Irani (2018) "Stereospecific proton exchange of glutathiohydroxyacetone by Glyoxalase I: A DFT study", Inorg. Chem., 57, 4944-4958; DOI 10.1021/acs.inorgchem.7b03215.
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.
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.
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.
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", Eur. Chem. J., 24, 10881-10905; DOI 10.1002/chem.201705952.
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.
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/s10822-018-0158-2; Open Access.
L. Cao, O. Caldararu, U. Ryde (2018) "Protonation and reduction of the FeMo cluster in nitrogenase studied by QM/MM calculations", J. Chem. Theory Comput., 14, 6653–6678; DOI 10.1021/acs.jctc.8b00778.
M. Wang, Y. Mei & U. Ryde (2018) "Predicting relative binding affinity using non-equilibrium QM/MM simulations", J. Chem. Theory Comput., 14, 6613-6622; DOI 10.1021/acs.jctc.8b00685.
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.
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.
L. Cao & U. Ryde (2019) "Extremely large differences in DFT energies for nitrogenase models", Phys. Chem. Chem. Phys., 21, 2480-248; DOI 10.1039/C8CP06930A; Open Access.
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., in press; DOI 10.1039/C8OB02888E; Open Access.
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., in press; DOI 10.1021/jacs.8b11099; Open Access.
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 J. Appl. Cryst., submitted 16/10-18; revised version submitted 28/1-19; accepted 30/1.
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., submitted 29/12-18.
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., submitted 2/1-19.
S. Jafari, U. Ryde, M. Irani (2019) "QM/MM study of the stereospecific proton exchange of glutathiohydroxyacetone by glyoxalase I", ACS Catal., submitted 7/1-19.
F. S. Alavi, N. Safari, U. Ryde, M. Zahedi (2019) "QM/MM study of the conversion of biliverdin into verdoheme by heme oxygenase", Chem. Phys. Lett., submitted 30/1-19.
20 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 (review articles).
10 286 citations in Web of Science, April 2018; h index 54.

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