Publications

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230.	O. Gracia Carmona, M. Lahham, P. Poliak, D. Goj, E. Frießer, S. Wallner, P. Macheroux, and C. Oostenbrink Understanding the riddle of amine oxidase flavoenzyme reactivity on the stereoisomers of N-methyl-dopa and N-methyl-tyrosine J. Mol. Recogn. (2023) online. doi: 10.1002/jmr.3068
229.	M. Barria-Urenda, A. Ruiz-Fernandez, C. Gonzalez, C. Oostenbrink, and J.A. Garate Size matters: free-energy calculations of amino acid adsorption over pristine graphene J. Chem. Inf. Model. (2023), online doi: 10.1021/acs.jcim.3c00418
228.	B. Motycka, F. Csarman, M. Rupp, K. Schnabel, G. Nagy, K. Karnpakdee, S. Scheiblbrandner, R. Tscheliessnig, C. Oostenbrink, M. Hammel and R. Ludwig Amino acid residues controlling domain interaction and interdomain electron transfer in cellobiose dehydrogenase ChemBioChem (2023) e202300431 doi: 10.1002/cbic.202300431
227.	O. Gracia Carmona and C. Oostenbrink Flexible Gaussian accelerated molecular dynamics to enhance biological sampling J. Chem. Theory Comput. (2023) online doi: 10.1021/acs.jctc.3c00619
226.	E. Galicia-Andrés, Y. Escalona, M. Gotsmy, C. Oostenbrink and D. Petrov Molecular Dynamics Simulations up to Earth: Modeling of Soil Organic Matter In "Reference Module in Chemistry, Molecular Sciences and Chemical Engineering; Comprehensive Computational Chemistry", Elsevier (2023) doi: 10.1016/B978-0-12-821978-2.00106-9
225.	O. Gracia Carmona, M. Gillhofer, L. Tomasiak, A. de Ruiter, C. Oostenbrink Accelerated enveloping distribution sampling to probe the presence of water molecules J. Chem. Theory Comput. (2023) online doi: 10.1021/acs.jctc.3c00109
224.	C. González-Fernández, C. Öhlknecht, M. Diem, Y. Escalona, E. Bringas, G. Moncalián, C. Oostenbrink and I. Ortiz Insights into the Binding Mode of Lipid A to the Anti-lipopolysaccharide Factor ALFPm3 from Penaeus monodon: An in Silico Study through MD Simulations J. Chem. Inf. Model. (2023) online doi: 10.1021/acs.jcim.3c00173
223.	Y. Escalona, D. Petrov, E. Galicia-Andrés and C. Oostenbrink Exploring the Macroscopic Properties of Humic Substances using Modeling and Molecular Simulations Agronomy 13 (2023) 1044 doi: 10.3390/agronomy13041044
222.	O. Gracia Carmona and C. Oostenbrink Accelerated Enveloping Distribution Sampling (AEDS) allows for efficient sampling of orthogonal degrees of freedom J. Chem. Inf. Model. (2022) online doi: 10.1021/acs.jcim.2c01272
221.	M.H. Gerzabek, D. Tunega, E. Galicia-Andrés and C. Oostenbrink Soil organic matter in molecular simulations. In "Reference Module in Earth Systems and Environmental Sciences; Encyclopedia of Soils in the Environment", Second Edition, Elsevier (2022) doi: 10.1016/B978-0-12-822974-3.00020-3
220.	H.R. Mansouri, O. Gracia Carmona, J. Jodlbauer, L. Schweiger, M.J. Fink, E. Breslmayr, C. Laurent, S. Feroz, L.C.P. Goncalves, D.V. Rial, M.D. Mihovilovic, A.S. Bommarius, R. Ludwig, C. Oostenbrink, F. Rudroff Mutations increasing cofactor affinity, improve stability and activity of a Baeyer−Villiger monooxygenase ACS Catal. 12 (2022) 11761 − 11766 doi: 10.1021/acscatal.2c03225
219.	C. González-Fernández, E. Bringas, C. Oostenbrink, I. Ortiz In Silico Investigation and Surmounting of Lipopolysaccharide Barrier in Gram-negative bacteria: How Far Has Molecular Dynamics Come? Comput. Struct. Biotechn. J. 20 (2022) 5886 - 5901 doi: 10.1016/j.csbj.2022.10.039
218.	J.F.W. Chan, Y.J. Oh, S. Yuan, H. Chu, M.L. Yeung, D. Canena, C.C.S. Chan, V.K.M. Poon, C.C.Y. Chan, A.J. Zhang, J.P. Cai, Z.W. Ye, L. Wen, T.T.T. Yuen, K.K.H. Chik, H. Shuai, Y. Wang, Y. Hou, C. Luo, W.M. Chan, Z. Qin, K.Y. Sit, W.K. Au, M. Legendre, R. Zhu, L. Hain, H. Seferovic, R. Tampé, K.K.W. To, K.H. Chan, D.G. Thomas, M. Klausberger, C. Xu, J.J. Moon, J. Stadlmann, J.M. Penninger, C. Oostenbrink, P. Hinterdorfer, K.Y. Yuen and D.M. Markovitz A molecularly engineered, broad-spectrum anti-coronavirus lectin inhibits SARS-CoV-2 and MERS-CoV infection in vivo Cell. Rep. Med. 3 (2022) 100774 doi: 10.1016/j.xcrm.2022.100774
217.	A. Wagner, E. Galicia-Andrés, M. Teufl, L. Gold, C. Obinger, P. Sykacek, C. Oostenbrink and M.W. Traxlmayr Identification of activating mutations in the transmembrane and extracellular domains of EGFR Biochemistry (2022), online doi: 10.1021/acs.biochem.2c00384
216.	P. Maleš, B. Pem, D. Petrov, D. Domazet Jurašin, and D. Bakarić Deciphering the origin of the melting profile of unilamellar phosphatidylcholine liposomes by measuring the turbidity of its suspensions Soft Matter 18 (2022) 6703-6715 doi: 10.1039/D2SM00878E
215.	N. Lingg, C. Kröß, P. Engele, C. Öhlknecht, C. Köppl, A. Fischer, B. Lier, J. Loibl, B. Sprenger, J. Liu, P. Scheidl, M. Berkemeyer, W. Buchinger, C. Brocard, G. Striedner, C. Oostenbrink, R. Schneider, A. Jungbauer, M. Cserjan-Puschmann CASPON platform technology: Ultrafast circularly permuted caspase-2 cleaves tagged fusion proteins before all 20 natural amino acids at the N-terminus New Biotechn. 71 (2022) 37-46 doi: 10.1016/j.nbt.2022.07.002
214.	V. Monteil, B. Eaton, E. Postnikova, M. Murphy, B. Braunsfeld, I. Crozier, F. Kricek, J. Niederhöfer, Alice Schwarzböck, H. Breid, A., S. Devignot, J. Klingström, C. Thålin, M.J. Kellner, W. Christ, S. Havervall, S. Mereiter, S. Knapp, A. Sanchez Jimenez, A. Bugajska-Schretter, A. Dohnal, C. Ruf, R. Gugenberger, A. Hagelkruys, N. Montserrat, I. Kozieradzki, O.H. Ali, J. Stadlmann, M.R. Holbrook, C. Schmaljohn, C. Oostenbrink, R.H. Shoemaker, A. Mirazimi, G. Wirnsberger and J.M. Penninger Clinical grade ACE2 as a universal agent to block SARS-CoV-2 variants EMBO Mol. Med. (2022), online doi: 10.15252/emmm.202115230
213.	E. Breslmayr, P. Poliak, A. Pozgajcic, R. Schindler, D. Kracher, C. Oostenbrink, R. Ludwig Inhibition of the Peroxygenase Lytic Polysaccharide Monooxygenase by Carboxylic Acids and Amino Acids Antioxidants 11 (2022) 1096 doi: 10.3390/antiox11061096
212.	B. Lier, P. Poliak, P. Marquetand, J. Westermayr, C. Oostenbrink BuRNN: Buffer Region Neural Network Approach for Polarizable-Embedding Neural Network/Molecular Mechanics Simulations J. Phys. Chem. Lett 13 (2022) 3812−3818 doi: 10.1021/acs.jpclett.2c00654
211.	Y. Escalona, N. Espinoza, M. Barría-Urenda, C. Oostenbrink, and J.A. Garate On the effects of induced polarizability at the water-graphene interface via classical charge-on-spring models Phys. Chem. Chem. Phys. 24 (2022) 7748–7758 doi:10.1039/D1CP05573A
210.	M.H. Gerzabek, A.J.A. Aquino, Y. Escalona, E. Galicia-Andrés, P. Grančič, C. Oostenbrink, D. Petrov, D. Tunega A contribution of molecular modeling to supramolecular structures in soil organic matter J. Plant Nutr. Soil Sci. 185 (2022) 44 - 59 doi: 10.1002/jpln.202100360
209.	R. Gawish, P. Starkl, L. Pimenov, A. Hladik, K. Lakovits, F. Oberndorfer, S.J.F. Cronin, A. Ohradanova-Repic, G. Wirnsberger, B. Agerer, L. Endler, T. Capraz, J.W. Perthold, D. Cikes, R. Koglgurber, A. Hagelkruys, N. Montserrat, A. Mirazimi, L. Boon, H. Stockinger, A. Bergthaler, C. Oostenbrink, J.M. Penninger and S. Knapp ACE2 is the critical in vivo receptor for SARS-CoV-2 in a novel COVID-19 mouse model with TNF- and IFNγ-driven immunopathology e-Life 11 (2022) e74623 doi: 10.7554/eLife.74623
208.	T. Capraz, N.F. Kienzl, E. Laurent, J.W. Perthold, E. Föderl-Höbenreich, C. Grünwald-Gruber, D. Maresch, V. Monteil, J. Niederhöfer, G. Wirnsberger, A. Mirazimi, K. Zatloukal, L. Mach, J.M. Penninger, C. Oostenbrink, J. Stadlmann Structure-guided glyco-engineering of ACE2 for improved potency as soluble SARS-CoV-2 decoy receptor eLife 10 (2021) e73641 doi: 10.7554/eLife.73641
207.	C. Kröß, P. Engele, B. Sprenger, A. Fischer, N. Lingg, M. Baier, C. Öhlknecht, B. Lier, C. Oostenbrink, M. Cserjan-Puschmann, G. Striedner, A. Jungbauer, R. Schneider PROFICS: A bacterial selection system for directed evolution of proteases J.Biol. Chem. 297 (2021) 101095 doi: 10.1016/j.jbc.2021.101095
206.	E. Galicia-Andrés, C. Oostenbrink, M.H. Gerzabek and D. Tunega On the adsorption mechanism of humic substances on kaolinite and their microscopic structure Minerals 11 (2021), 1138 doi: 10.3390/min11101138
205.	J.E. Hernandez Gonzalez, E. Salas-Sarduy, L. Hernández Alvarez, D.E. Barreto Gomes, P.G. Pascutti, C. Oostenbrink, V.B.P. Leite In silico identification of noncompetitive inhibitors targeting an uncharacterized allosteric site of falcipain-2 J. Comput-Aid.. Mol. Des. 35 (2021) 1067 - 1079 doi: 10.1007/s10822-021-00420-7
204.	C. González-Fernández, A. Basauri, M. Fallanza, E. Bringas, C. Oostenbrink and I. Ortiz Fighting Against Bacterial LPS Caused Infections through Molecular Dynamics Simulations: A Review J. Chem. Inf. Model. 61 (2021) 4839–4851 doi: 10.1021/acs.jcim.1c00613
203.	D. Petrov Perturbation Free-Energy Toolkit: An Automated Alchemical Topology Builder J. Chem. Inf. Model. 61 (2021) 4382–4390 doi: 10.1021/acs.jcim.1c00428
202.	F. Sebastiani, H. Michlits, B. Lier, M. Becucci, P.G. Furtmüller, C. Oostenbrink, C. Obinger, S. Hofbauer, and G. Smulevich Reaction intermediate rotation during the decarboxylation of coproheme to heme b in C. diphtheriae Biophys J. 120 (2021) 3600-3614 doi: 10.1016/j.bpj.2021.06.042
201.	D. Hoffmann, S. Mereiter, Y.J. Oh, V. Monteil, E. Elder, R. Zhu, D. Canena, L. Hain, E. Laurent, C. Grünwald-Gruber, M. Klausberger, G. Jonsson, M.J. Kellner, M. Novatchkova, M. Ticevic, A. Chabloz, G. Wirnsberger, A. Hagelkruys, F. Altmann, L. Mach, J. Stadlmann, C. Oostenbrink, A. Mirazimi, P. Hinterdorfer and J.M. Penninger Identification of lectin receptors for conserved SARS-CoV-2 glycosylation sites EMBO J. 40 (2021) e108375 doi: 10.15252/embj.2021108375
200.	E. Galicia-Andrés, P. Grančič, M.H. Gerzabek, C. Oostenbrink, and D. Tunega Modeling of interactions in natural and synthetic organoclays In "Computational modeling in Clay Mineralogy", AIPEA, Ed. I. Sainz Díaz (2021), pp. 211 - 253 doi: 10.14644/AES.003
199.	E. Galicia-Andrés, Y. Escalona, C. Oostenbrink, D. Tunega, M.H. Gerzabek Soil organic matter stabilization at molecular scale: the role of metal cations and hydrogen bonds Geoderma 401 (2021) 115237 doi: 10.1016/j.geoderma.2021.115237
198.	Y. Escalona, D. Petrov and C. Oostenbrink Changes in Macroscopic Properties due to Microscopic Changes Geochim. Cosmochim. Acta 307 (2021) 228-241 doi: 10.1016/j.gca.2021.05.035
197.	M. Pechlaner, C. Oostenbrink and W.F. van Gunsteren On the use of multiple-time-step algorithms to save computing effort in molecular dynamics simulations of proteins J. Comput. Chem. 42 (2021) 1263–1282 doi: 10.1002/jcc.26541
196.	M. Gotsmy, Y. Escalona, C. Oostenbrink, D. Petrov Exploring the structure and dynamics of proteins in soil organic matter Proteins 89 (2021) 925 - 936 doi: 10.1002/prot.26070
195.	C. Öhlknecht, S. Katz, C. Kröß, B. Sprenger, P. Engele, R. Schneider, C. Oostenbrink Efficient in-silico saturation mutagenesis of a member of the Caspase protease family J. Chem. Inf. Model. 61 (2021) 1193–1203 doi: 10.1021/acs.jcim.0c01216
194.	W.F. van Gunsteren, X. Daura, P.F.J. Fuchs, N. Hansen, B.A.C. Horta, P.H. Hünenberger, A.E. Mark, M. Pechlaner, S. Riniker, and C. Oostenbrink On the Effect of the Various Assumptions and Approximations used in Molecular Simulation on the Properties of Bio-Molecular Systems: A Review of Issues ChemPhysChem 22 (2021) 264-282 doi: 10.1002/cphc.202000968
193.	A.K.G. Felice, C. Schuster, A. Kadek, F. Filandr, C.V.F.P. Laurent, S. Scheiblbrandner, L. Schwaiger, F. Schachinger, D. Kracher, C. Sygmund, P. Man, P. Halada, C. Oostenbrink and R. Ludwig Chimeric cellobiose dehydrogenases reveal the function of cytochrome domain mobility for the electron transfer to lytic polysaccharide monooxygenase ACS Catalysis 11 (2021) 517−532 doi: 10.1021/acscatal.0c05294
192.	B. Lier, C. Öhlknecht, A. de Ruiter, J. Gebhardt, W.F. van Gunsteren, C. Oostenbrink, N. Hansen A Suite of Advanced Tutorials for the GROMOS Biomolecular Simulation Software [Article v1.0] Living J. Comp. Mol. Sci. 2 (2020) 18552 doi: 10.33011/livecoms.2.1.18552
191.	A. de Ruiter, D. Petrov and C. Oostenbrink Optimization of alchemical pathways using extended thermodynamic integration J. Chem. Theory Comput. 17 (2021) 56–65 doi: 10.1021/acs.jctc.0c01170
190.	B. Roither, C. Oostenbrink, G. PFeiler, H. Koelbl, W. Schreiner Pembrolizumab induces an unexpected conformational change in the CC'-loop of PD-1 Cancers 13 (2021), 5 doi: 10.3390/cancers13010005
189.	B. Roither, C. Oostenbrink, W. Schreiner Molecular dynamics of the immune checkpoint programmed cell death protein I, PD-1: conformational changes of the BC-loop upon binding of the ligand PD-L1 and the monoclonal antibody nivolumab BMC Bioinformatics 21 (Suppl 17) (2020) 557 doi: 10.1186/s12859-020-03904-9
188.	Y. Escalona, D. Petrov and C. Oostenbrink Vienna Soil Organic Matter Modeler 2 (VSOMM2) J. Mol. Graph. Model. 103 (2021) 107817 doi: 10.1016/j.jmgm.2020.107817
187.	M. Cserjan-Puschmann, N. Lingg, P. Engele, C. Kröß, J. Loibl, A. Fischer, F. Bacher, A.C. Frank, C. Öhlknecht, C. Brocard, C. Oostenbrink, M. Berkemeyer, R. Schneider, G. Striedner, A. Jungbauer Production of Circularly Permuted Caspase-2 for Affinity Fusion-tag Removal: Cloning, Expression in Escherichia coli, Purification and Characterization Biomolecules 10 (2020), 1592 doi: 10.3390/biom10121592
186.	C. Öhlknecht, J.W. Perthold, B. Lier, C. Oostenbrink Charge-changing perturbations and path sampling via classical molecular dynamics simulations of simple guest-host systems J. Chem. Theory Comput. 16 (2020) 7721−7734 doi: 10.1021/acs.jctc.0c00719
185.	N. Lingg, C. Öhlknecht, A. Fischer, M. Mozgovicz, T. Scharl, C. Oostenbrink, A. Jungbauer Proteomics analysis of host cell proteins after immobilized metal affinity chromatography: influence of ligand and metal ions J. Chromatogr. A 1633 (2020) 461649 doi: 10.1016/j.chroma.2020.461649
184.	M. Diem, C. Oostenbrink The effect of different cutoff schemes in molecular simulations of proteins J. Comput. Chem. 41 (2020) 2740 - 2749 doi: 10.1002/jcc.26426
183.	M. Diem and C. Oostenbrink The effect of using a twin-range cut-off scheme for non-bonded interactions: Implications for force-field parameterization? J. Chem. Theory Comput. 16 (2020) 5985−5990 doi: 10.1021/acs.jctc.0c00509
182.	S. Yang, J.D.H. Liu, M. Diem, S. Wesseling, J. Vervoort, C. Oostenbrink, I.M.C.M. Rietjens Molecular dynamics and in vitro quantification of safrole DNA adducts reveal DNA adduct persistence due to limited DNA distortion resulting in inefficient repair Chem. Res. Toxicol. 33 (2020) 2298−2309 doi: 10.1021/acs.chemrestox.0c00097
181.	J.W. Perthold, D. Petrov, C. Oostenbrink Towards Automated Free Energy Calculation with Accelerated Enveloping Distribution Sampling (AEDS) J. Chem. Inf. Model. 60 (2020) 5395 - 5406 doi: 10.1021/acs.jcim.0c00456
180.	C. Ohlknecht, D. Petrov, P. Engele, C. Kröß, B. Sprenger, A. Fischer, N. Lingg, R. Schneider, C. Oostenbrink Enhancing the promiscuity of a member of the Caspase protease family by rational design Proteins 88 (2020) 1303 - 1318 doi: 10.1002/prot.25950
179.	E. Galicia-Andrés, D. Tunega, M.H. Gerzabek, C. Oostenbrink On glyphosate–kaolinite surface interactions. A molecular dynamic study Eur. J. Soil Sci. 72 (2021) 1231 - 1242 doi: 10.1111/ejss.12971
178.	H. Michlits, B. Lier, V. Pfanzagl, K. Djinović-Carugo, P.G. Furtmüller, C. Oostenbrink, C. Obinger, S. Hofbauer Actinobacterial coproheme decarboxylases use histidine as distal base to promote Compound I formation ACS Catal. 10 (2020), 5405−5418 doi: 10.1021/acscatal.0c00411
177.	E. Breslmayr, C.V.F.P. Laurent, S. Scheiblbrandner, A. Jerkovic, D.J. Heyes, C. Oostenbrink, R. Ludwig, T.M. Hedison, N.S. Scrutton, D. Kracher Protein Conformational Change is Essential For Reductive Activation of Lytic Polysaccharide Monooxygenase by Cellobiose Dehydrogenase ACS Catalysis 10 (2020), 4841 - 4853 doi: 10.1021/acscatal.0c00754
176.	S. Yang, M. Diem, D.H. Liu, S. Wesseling, J. Vervoort, C. Oostenbrink, I.M.C.M. Rietjens Cellular levels and molecular dynamics simulations of estragole DNA adducts point at inefficient repair resulting from limited distortion of the double stranded DNA helix Arch. Toxicol 94 (2020) 1349–1365 doi: 10.1007/s00204-020-02695-5
175.	M. Gladovic, C. Oostenbrink, U. Bren Could microwave irradiation cause misfolding of peptides? J. Chem. Theory Comput. 16 (2020) 2795 - 2802 doi: 10.1021/acs.jctc.9b01104
174.	A. de Ruiter and C. Oostenbrink Advances in the calculation of binding free energies Curr. Opin. Struct. Biol. 61 (2020) 207 - 212 doi: 10.1016/j.sbi.2020.01.016
173.	C. Öhlknecht, B. Lier, D. Petrov, J. Fuchs and C. Oostenbrink Correcting electrostatic artifacts due to net-charge changes in the calculation of ligand binding free energies J. Comput. Chem. 41 (2020) 986–999 doi: 10.1002/jcc.26143
172.	M. Diem and C. Oostenbrink Hamiltonian Reweighing to refine Protein Backbone Dihedral-Angle Parameters in the GROMOS Force Field J. Chem. Inf. Model. 60 (2020) 279 - 288 doi: 10.1021/acs.jcim.9b01034
171.	A. Turupcu, M. Blaukopf, P. Kosma and C. Oostenbrink Molecular conformations of di-, tri-, and tetra-α-(2→8)-linked sialic acid from NMR spectroscopy and MD simulations Int. J. Mol. Sci. 21 (2020) 30 doi:10.3390/ijms21010030
170.	C.V.F.P. Laurent, P. Sun, S. Scheiblbrandner, F. Csarman, P. Cannazza, M. Frommhagen, W.J.H. van Berkel, C. Oostenbrink, M.A. Kabel and R. Ludwig Influence of Lytic Polysaccharide Monooxygenase Active Site Segments on Activity and Affinity Int. J. Mol. Sci. 20 (2019), 6219 doi: 10.3390/ijms20246219
169.	E. Breslmayr, S. Daly, A. Požgajčić, H. Chang, T. Rezić, C. Oostenbrink and Roland Ludwig Improved Spectrophotometric Assay for Lytic Polysaccharide Monooxygenase Biotechnol. Biofuel. 12 (2019)283 doi: 10.1186/s13068-019-1624-3
168.	J.W. Perthold and C. Oostenbrink GroScore: Accurate scoring of protein-protein binding poses using explicit-solvent free-energy calculations J. Chem. Inf. Model. 59 (2019) 5074 - 5085 doi: 10.1021/acs.jcim.9b00687
167.	E. Galicia-Andrés, D. Petrov, M.H. Gerzabek, C. Oostenbrink and D. Tunega Polarization effects in simulations of kaolinite-water interfaces Langmuir 35 (2019) 15086 - 15099 doi: 10.1021/acs.langmuir.9b02945
166.	M. Maurer and C. Oostenbrink Water in Protein Hydration and Ligand Recognition J. Mol. Recogn. 32 (2019), e2810 doi: 10.1002/jmr.2810
165.	D. Petrov, D. Tunega, M.H. Gerzabek, C. Oostenbrink Molecular modeling of sorption processes of a range of diverse small organic molecules in Leonardite humic acid Eur. J. Soil Sci. 71 (2020) 831 - 844 doi: 10.1111/ejss.12868
164.	A. Turupcu, P. Poliak, C. Margreitter, C. Oostenbrink, E. Staudacher UDP-N-acetyl-α-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase from the snail Biomphalaria glabrata – structural reflections Glycoconjugate J. 37 (2020) 15 - 25 doi: 10.1007/s10719-019-09886-y
163.	K. Göritzer, A. Turupcu, D. Maresch, J. Novak, F. Altmann, C. Oostenbrink, C. Obinger, R. Strasser Distinct Fc alpha receptor N-glycans modulate the binding affinity to IgA J. Biol. Chem. 294 (2019) 13995 - 14008 doi: 10.1074/jbc.RA119.009954
162.	L. Schwaigerlehner, P. Mayrhofer, M. Diem, W. Steinfellner, E. Fenech, C. Oostenbrink, R. Kunert Germinality does not necessarily define mAb expression and thermal stability Appl. Microbiol. Biotechn. 103 (2019) 7505–7518 doi: 10.1007/s00253-019-09998-3
161.	A. Turupcu, A.M. Bowen, A. Di Paolo, A. Matagne, C. Oostenbrink, C. Redfield, and L.J. Smith The Dynamics of Bacteriophage Lambda Lysozyme in Complex with Hexa- and Tetra-N-acetylchitohexaose investigated by NMR and MD Simulations Proteins 88 (2020) 82 - 93 doi: 10.1002/prot.25770
160.	V. Pfanzagl, M. Bellei, S. Hofbauer, C.V.F.P. Laurent, P.G. Furtmüller, C. Oostenbrink, G. Battistuzzi, C. Obinger Redox thermodynamics of B-class dye-decolorizing peroxidases J. Inorg. Biochem. 199 (2019) 110761 doi: 10.1016/j.jinorgbio.2019.110761
159.	S. Ma, C.V.F.P. Laurent, M. Meneghello, J. Tuoriniemi, C. Oostenbrink, L. Gorton, P.N. Bartlett, Roland Ludwig Direct electron transfer anisotropy of site-specifically immobilized cellobiose dehydrogenase ACS Catalysis 9 (2019) 7607−7615 DOI: 10.1021/acscatal.9b02014
158.	Z. Jandova, W. Jespers, E. Sotelo, H. Gutiérrez de Terán and C. Oostenbrink Free-energy calculations for Bioisosteric Modifications of A3 adenosine receptor antagonists Int. J. Mol. Sci. 20 (2019) 3499 doi: 10.3390/ijms20143499
157.	L. Milazzo, T. Gabler, D. Pühringer, Z. Jandova, D. Maresch, H. Michlits, V. Pfanzagl, K. Djinović-Carugo, C. Oostenbrink, P.G. Furtmüller, C. Obinger, G. Smulevich, S. Hofbauer Redox cofactor twists during its stewise decarboxylation - molecular mechanism of conversion of coproheme to heme b ACS Catal. 9 (2019) 6766 - 6782 doi: 10.1021/acscatal.9b00963
156.	Z. Jandova, S.C. Gill, N.M. Lim, D.L. Mobley, C. Oostenbrink Binding modes and metabolism of caffeine Chem. Res. Toxicol. 32 (2019) 1374 - 1383 doi: 10.1021/acs.chemrestox.9b00030
155.	A. Turupcu, M. Diem, L.J. Smith, C. Oostenbrink Structural aspects of the O-glycosylation linkage via MD simulations and comparison with NMR experiments ChemPhysChem 20 (2019) 1527 - 1537 doi: 10.1002/cphc.201900079
154.	D. Vila-Vicosa, P.B. P. S. Reis, A.M. Baptista, C. Oostenbrink and M. Machuqueiro A pH replica exchange scheme in the stochastic titration constant-pH MD method (RESTCpH) J. Chem. Theory Comput. 15 (2019) 3108 - 3116 doi: 10.1021/acs.jctc.9b00030
153.	C.V.F.P. Laurent, E. Breslmayr, D. Tunega, R. Ludwig and C. Oostenbrink The interaction between cellobiose dehydrogenase and lytic polysaccharide monooxygenase Biochemistry 58 (2019) 1226-1235 doi: 10.1021/acs.biochem.8b01178
152.	W. Hohlweg, G.E. Wagner, H.F. Hofbauer, F. Sarkleti, M. Setz, N. Gubensäk, S. Lichtenegger, S.F. Falsone, H. Wolinski, S. Kosol, C. Oostenbrink, S.D. Kohlwein, and K. Zangger A cation-π interaction in a transmembrane helix of vacuolar ATPase retains the proton transporting arginine in a hydrophobic environment J. Biol. Chem. 293 (2018) 18977–18988 doi: 10.1074/jbc.RA118.005276
151.	T.F.D. Silva, D. Vila-Vicosa, P.B.P.S. Reis, B.L. Victor, M. Diem, C. Oostenbrink and M. Machuqueiro The impact of using single atomistic long range cutoff schemes with the GROMOS 54A7 force field J. Chem. Theory Comput. 14 (2018) 5823 - 5833 doi: 10.1021/acs.jctc.8b00758
150.	M. Maurer, N. Hansen and C. Oostenbrink Comparison of Free-Energy Methods Using a Tripeptide-Water Model System J. Comput. Chem. 39 (2018) 2226 - 2242 doi: 10.1002/jcc.25537
149.	A. Turupcu, W. Almohamed, C. Oostenbrink and G.J. Seifert A speculation on the tandem fasciclin 1 repeat of FLA4 proteins in angiosperms Plant Signal. Behav. 13 (2018) e1507403 doi: 10.1080/15592324.2018.1507403
148.	A. Porodko, A. Cirnski, D. Petrov, T. Mayer, M. Paireder, B. Mayer, D. Maresch, L. Nika, M.L. Biniossek, P. Gallois, O. Schilling, C. Oostenbrink, M. Novinec, L. Mach The two cathepsin B-like proteases of Arabidopsis thaliana are closely related enzymes with discrete endopeptidase and carboxydipeptidase activities Biol. Chem. 399 (2018) 1223 - 1235 doi: 10.1515/hsz-2018-0186
147.	L. Schwaigerlehner, M. Pechlaner, P. Mayrhofer, C. Oostenbrink, R. Kunert Lessons learned from merging wet lab experiments with molecular simulation to improve mAb humanization Protein Eng. Des. Sel. 31 (2018) 257 - 265 doi: 10.1093/protein/gzy009
146.	J.W. Perthold and C. Oostenbrink Accelerated enveloping distribution sampling: enabling sampling of multiple end-states while preserving local energy minima J. Phys. Chem. B 122 (2018) 5030 - 5037 doi: 10.1021/acs.jpcb.8b02725
145.	E. Breslmayr, M. Hanžek, A. Hanrahan, C. Leitner, R. Kittl, B. Šantek, C. Oostenbrink, R. Ludwig A fast and sensitive activity assay for lytic polysaccharide monooxygenase Biotechnol. Biofuel 11 (2018) 79 doi: 10.1186/s13068-018-1063-6
144.	Z. Jandova, D. Fast, M. Setz, M. Pechlaner, C. Oostenbrink Saturation mutagenesis by efficient free-energy calculation J. Chem. Theory Comput. 14 (2018) 894 - 904 doi: 10.1021/acs.jctc.7b01099
143.	D. Bakaric, D. Petrov, Y. Kunhi Mouvenchery, S. Heiβler, C. Oostenbrink, G.E. Schaumann Ion-induced modification of the sucrose network and its impact on melting of freeze-dried liposomes. DSC and molecular dynamics study Chem. Phys. Lipids 210 (2018) 38 - 46 doi: 10.1016/j.chemphyslip.2017.11.015
142.	EE. Németh, M. Noby Asaka, K. Kato, Z. Fábián, C. Oostenbrink, H.E.M. Christensen, K. Nagata, and B. Gyurcsik Chemical approach to biological safety - Molecular level control of an integrated zinc finger nuclease ChemBioChem 19 (2018) 66 - 75 doi: 10.1002/cbic.201700420
141.	W.F. van Gunsteren, X. Daura, N. Hansen, A.E. Mark, C. Oostenbrink, S.Riniker, and L.J. Smith Validation of molecular simulation: an overview of issues Angew. Chem. Intl. Ed., 57 (2018) 884 - 902 doi: 10.1002/anie.201702945 Angew. Chem. 130 (2018) 894 - 915 doi: 10.1002/ange.201702945
140.	Z. Jandova, Z. Trosanova, V. Weisova, C. Oostenbrink, J. Hritz Free energy calculations on the stability of the 14-3-3ζ protein BBA - Proteins and Proteomics 1866 (2017) 442 - 450 doi: 10.1016/j.bbapap.2017.11.012
139.	J.W. Perthold and C. Oostenbrink Simulation of Reversible Protein-Protein Binding and Calculation of Binding Free Energies using Perturbed Distance Restraints J. Chem. Theory Comput. 13 (2017) 5697 - 5708 doi: 10.1021/acs.jctc.7b00706
138.	A. Turupcu and C. Oostenbrink Modeling of oligosaccharides within glycoproteins from free-energy landscapes J. Chem. Inf. Model. 57 (2017) 2222 - 2236 doi: 10.1021/acs.jcim.7b00351
137.	G. Nagy, C. Oostenbrink and J. Hritz Exploring the Binding Pathways of the 14-3-3ζ Protein: Structural and free-energy profiles revealed by Hamiltonian Replica Exchange Molecular Dynamics with distance field distance restraints PLoS ONE 12 (2017), e0180633 doi: 10.1371/journal.pone.0180633
136.	K. Sergelen, S. Fossati, A. Turupcu, C. Oostenbrink, B. Liedberg, W.Knoll, and J. Dostálek Plasmon field-enhanced fluorescence energy transfer for loop aptamer assay readout ACS Sens. 2 (2017) 916 - 923 doi: 10.1021/acssensors.7b00131
135.	L. Montero-Morales, D. Maresch, A. Castilho, A. Turupcu, K. Ilieva, S. Crescioli, S. Karagiannis, C. Lupinek, C. Oostenbrink, F. Altmann, H. Steinkellner Recombinant plant-derived human IgE glycoproteomics J. Proteom. 161 (2017) 81 - 87 doi: 10.1016/j.jprot.2017.04.002
134.	D. Petrov, D. Tunega, M.H. Gerzabek, C. Oostenbrink Molecular dynamics simulations of the standard Leonardite humic acid: microscopic analysis of the structure and dynamics Env. Sci. Techn. 51 (2017) 5414 - 5424 doi: 10.1021/acs.est.7b00266
133.	C. Margreitter and C. Oostenbrink MDplot: Visualise Molecular Dynamics The R Journal 9 (2017), 164 - 186 https://journal.r-project.org/archive/2017/RJ-2017-007/index.html
132.	I. Grishkovskaya, M. Paumann-Page, R. Tscheliessnig, J.a Stampler, S.Hofbauer, M. Soudi, B. Sevcnikar, C. Oostenbrink, P.G. Furtmüller, K. Djinović-Carugo, W.M. Nauseef and C. Obinger Structure of human promyeloperoxidase (proMPO) and the role of the propeptide for processing and maturation J. Biol. Chem., 292 (2017) 8244 - 8261 doi: 10.1074/jbc.M117.775031
131.	C. Margreitter, M.M. Reif and C. Oostenbrink Update on phosphate and charged post-translationally modified amino acid parameters in the GROMOS force field J. Comput. Chem. 38 (2017) 714 – 720 doi: 10.1002/jcc.24733
130.	M. Pechlaner, M. Reif, C. Oostenbrink Reparametrization of United-Atom Amine Solvation in the GROMOS Force Field Mol. Phys. 115 (2017) 1144 - 1154 doi: 10.1080/00268976.2016.1255797
129.	W. F. van Gunsteren, J. R. Allison, X. Daura, J. Dolenc, N. Hansen, A.E. Mark, C. Oostenbrink, V. H. Rusu, L. J. Smith Deriving structural information from experimentally measured data on biomolecules Angew. Chem. 128 (2016) 16222 – 16244 doi:10.1002/ange.201601828 Angew. Chem. Int. Ed. 55 (2016) 15990 – 16010 doi: 10.1002/anie.201601828
128.	J. van Leeuwen, C. Pons, J.C. Mellor, T.N. Yamaguchi, H. Friesen, J. Koschwanez, M. Mattiazzi Ušaj, M. Pechlaner, M. Takar, M. Ušaj, B. VanderSluis, K. Andrusiak, P. Bansal, A. Baryshnikova, C. Boone, J. Cao, A. Cote, M. Gebbia, G. Horecka, I. Horecka, E. Kuzmin, N. Legro, W. Liang, N. van Lieshout, M. McNee, B.-J. San Luis, F. Shaeri, E. Shuteriqi, S. Sun, L. Yang, J.-Y. Youn, M. Yuen, M. Costanzo, A.-C. Gingras, P. Aloy, C. Oostenbrink, A. Murray, T.R. Graham, C.L. Myers, B.J. Andrews, F.P. Roth, and C. Boone Exploring Genetic Suppression Interactions on a Global Scale Science 354 (2016), aag0839 doi: 10.1126/science.aag0839
127.	M.M.H. Graf, M. Maurer, and C. Oostenbrink Free-energy calculations of residue mutations in a tripeptide using various methods to overcome inefficient sampling J. Comput. Chem. 37 (2016), 2597 - 2605 doi: 10.1002/jcc.24488
126.	S. Hofbauer, M. Dalla Sega, S. Scheiblbrandner, Z. Jandova, I. Schaffner, G. Mlynek, K. Djinovic-Carugo, G. Battistuzzi, P.G. Furtmüller, C. Oostenbrink, C. Obinger Chemistry and molecular dynamics simulations of heme b-HemQ and coproheme-HemQ Biochemistry 55 (2016), 5398–5412 doi: 10.1021/acs.biochem.6b00701
125.	C. Margreitter and C. Oostenbrink On the optimization of the protein backbone dihedral angles by means of Hamiltonian reweighting J. Chem. Inf. Model. 56 (2016) 1823 - 1834 doi: 10.1021/acs.jcim.6b00399 Erratum: J. Chem. Inf. Model. 58 (2018) 1716−1720 doi: 10.1021/acs.jcim.8b00470
124.	A. de Ruiter and C. Oostenbrink Extended Thermodynamic Integration: efficient prediction of lambda derivatives at non-simulated points J. Chem. Theory Comput. 12 (2016) 4476 - 4486 doi: 10.1021/acs.jctc.6b00458
123.	B. Gasselhuber, M.M.H. Graf, C. Jakopitsch, M. Zamocky, A. Nicolussi, P.G. Furtmüller, C. Oostenbrink, X. Carpena and C. Obinger Interaction with the redox cofactor MYW and functional role of a mobile arginine in eukaryotic catalase-peroxidase Biochemistry 55 (2016), 3528 - 3541 doi: 10.1021/acs.biochem.6b00436
122.	M. Maurer, S.B.A. de Beer and C. Oostenbrink Calculation of relative binding free energy in the water-filled active site of oligopeptide-binding protein A Molecules 21 (2016), 499 doi: 10.3390/molecules21040499
121.	C. Margreitter, P. Mayrhofer, R. Kunert and C. Oostenbrink Antibody humanization by molecular dynamics simulations – in-silico guided selection of critical backmutations J. Mol. Recogn. 29 (2016) 266 - 275 doi: 10.1002/jmr.2527
120.	L. Olsen, F.S. Jørgensen and C. Oostenbrink Cytochrome P450 Mediated Drug Metabolism In "New Horizons in Predictive Drug Metabolism and Pharmacokinetics", Ed. A.G.E. Wilson, Royal Society of Chemistry, Cambridge (2016), pp. 66 - 78 doi: 10.1039/9781782622376-00066
119.	M. Pechlaner and C. Oostenbrink Multiple binding poses in the hydrophobic cavity of bee odorant binding protein AmelOBP14 J. Chem. Inf. Model 55 (2015) 2633 - 2643 doi: 10.1021/acs.jcim.5b00673
118.	A. Sündermann, R. Solc, D. Tunega, G. Haberhauer, M.H. Gerzabek, C. Oostenbrink Vienna Soil Organic Matter Modeler - Generating condensed-phase models of humic substances J. Mol. Graph. Model. 62 (2015) 243 - 261 doi: 10.1016/j.jmgm.2015.10.007
117.	B. Gasselhuber, X. Carpena, M.M.H. Graf, K.F. Pirker, A. Nicolussi, A. Sündermann, S. Hofbauer, M. Zamocky, P.G. Furtmüller, C. Jakopitsch, C. Oostenbrink, I. Fita and C. Obinger Eukaryotic catalase-peroxidase: the role of the Trp-Tyr-Met adduct in protein stability, substrate accessibility and catalysis of hydrogen peroxide dismutation Biochemistry 54 (2015) 5425 - 5438 doi: 10.1021/acs.biochem.5b00831
116.	M. Graf, J. Sucharitakul, U. Bren, B. Chu, G. Köllensberger, S. Hann, P. Furtmüller, C. Obinger, C. Peterbauer, C. Oostenbrink, P. Chaiyen, D. Haltrich Reaction of pyranose dehydrogenase from Agaricus meleagris with its carbohydrate substrates FEBS Journal 282 (2015) 4218 – 4241 doi: 10.1111/febs.13417
115.	L. Olsen, C. Oostenbrink, F.S. Jørgensen Prediction of cytochrome P450 mediated metabolism Adv. Drug Deliv. Rev. 86 (2015) 61 - 71 doi: 10.1016/j.addr.2015.04.020
114.	A. Castilho, C. Gruber, A. Thader, C. Oostenbrink, M. Pechlaner, H. Steinkellner, F. Altmann Processing of complex N-glycans in IgG Fc-region is affected by core-fucosylation mAbs 7 (2015), 863 - 870 doi: 10.1080/19420862.2015.1053683
113.	M. Grandits, A. Sündermann and C. Oostenbrink LUCI4HPC Linux Journal 252 (2015), 68 - 76
112.	M. Grandits and C. Oostenbrink Selectivity of cytosolic phospholipase A2 type IV towards arachidonyl phospholipids J. Mol. Recogn., 28 (2015) 447 - 457 doi: 10.1002/jmr.2462
111.	B. Zolghadr, B. Gasselhuber, M. Windwarder, M. Pabst, D. Kracher, M. Kerndl, S. Zayni, A. Hofinger-Horvath, R. Ludwig, D. Haltrich, C. Oostenbrink, C. Obinger, P. Kosma, P. Messner, and C. Schäffer UDP-Sulfoquinovose Formation by Sulfolobus acidocaldarius Extremophiles 19 (2015) 451 - 467 doi: 10.1007/s00792-015-0730-9
110.	M.M. Reif and C. Oostenbrink Towards the correction of effective electrostatic forces in explicit-solvent molecular dynamics simulations: Restraints on solvent-generated electrostatic potential and solvent polarization Theor. Chem. Acc. 134 (2015) 2 doi: 10.1007/s00214-014-1600-8
109.	J.A. Garate, J. Stöckl, M. del Carmen Fernández-Alonso, D. Artner, M. Haegman, C. Oostenbrink, J. Jiménez-Barbero, R. Beyaert, H. Heine, P. Kosma, and A. Zamyatina Anti-endotoxic Activity and Structural basis for human MD-2·TLR4 Antagonism of Tetraacylated Lipid A Mimetics based on beta-GlcN(1↔1)alpha-GlcN Scaffold Innate Immun. 21 (2015) 490 - 503 doi: 10.1177/1753425914550426
108.	M. M. H. Graf, Z. Lin, U. Bren, D. Haltrich, W. F. van Gunsteren, and C. Oostenbrink Pyranose Dehydrogenase Ligand Promiscuity: A Generalized Approach to Simulate Monosaccharide Solvation, Binding, and Product Formation PLOS Comput. Biol. 10 (2014) e1003995 doi: 10.1371/journal.pcbi.1003995
107.	A.B. Nørholm, P. Francotte, E. Goffin, I. Botez, L. Danober, P. Lestage, B. Pirotte, J.S. Kastrup, L. Olsen, and C. Oostenbrink Thermodynamic characterization of new positive allosteric modulators binding to the glutamate receptor A2 ligand-binding domain: combining experimental and computational methods unravels differences in driving forces J. Chem. Inf. Model 54 (2014) 3404−3416 doi: 10.1021/ci500559b
106.	U. Bren, J.E. Fuchs and C. Oostenbrink Cooperative Binding of Aflatoxin B1 by Cytochrome P450 3A4: A Computational Study Chem. Res. Toxicol. 27 (2014) 2136−2147 doi: 10.1021/tx5004062
105.	M.M. Reif and C. Oostenbrink Molecular dynamics simulation of configurational ensembles compatible with experimental FRET efficiency data through a restraint on instantaneous FRET efficiencies J. Comput. Chem. 35 (2014) 2319 - 2332 doi: 10.1002/jcc.23756
104.	C.Oostenbrink Structure-based methods for predicting the sites and products of metabolism In "Drug Metabolism Prediction", Ed. J. Kirchmair, Wiley, Weinheim (2014), pp. 243 - 263
103.	M. Grandits and C. Oostenbrink Molecular dynamics simulations of the Auxin Binding Protein 1 in complex with indole-3-acetic acid and naphthalen-1-acetic acid Proteins 82 (2014) 2744 - 2755 doi: 10.1002/prot.24639
102.	A. Sündermann, M.M. Reif, S. Hofbauer, C. Obinger and C. Oostenbrink Investigation of ion binding in chlorite dismutases by means of molecular dynamics simulations Biochemistry 53 (2014) 4869 - 4879 doi: 10.1021/bi500467h
101.	M.W. Traxlmayr, E. Lobner, C. Hasenhindl, G. Stadlmayr, C. Oostenbrink, F. Rüker and C. Obinger Construction of pH-sensitive Her2-binding IgG1-Fc by directed evolution Biotechnol. J. 9 (2014) 1013 - 1022 doi: 10.1002/biot.201300483
100.	E. Németh, G.K. Schilli, G. Nagy, C. Hasenhindl, B. Gyurcsik, C. Oostenbrink Design of a colicin E7 based chimeric zinc-finger nuclease J. Comp.-Aided Mol. Des. 28 (2014) 841 - 850 doi: 10.1007/s10822-014-9765-8
99.	C. Hasenhindl, B. Lai, J. Delgado, M. W. Traxlmayr, G. Stadlmayr, F. Rüker, L. Serrano, C. Oostenbrink, C. Obinger Creating stable stem regions for loop elongation in Fcabs – Insights from combining yeast surface display, in silico loop reconstruction and molecular dynamics simulations Biochim. Biophys. Acta 1844 (2014) 1530 - 1540 doi: 10.1016/j.bbapap.2014.04.020
98.	S. Hofbauer, C. Gruber, K.F. Pirker, A. Sündermann, I. Schaffner, C. Jakopitsch, C. Oostenbrink, P.G. Furtmüller, C. Obinger Transiently produced hypochlorite is responsible for the irreversible inhibition of chlorite dismutase Biochemistry 53 (2014) 3145 - 3157 doi: 10.1021/bi500401k
97.	A. Loos, C. Gruber, F. Altmann, U. Mehofer, F. Hensel, M. Grandits, C. Oostenbrink, G. Stadlmayr, P.G. Furtmüller, and H. Steinkellner Expression and glycoengineering of functionally active hetero-multimeric IgM in plants Proc. Natl. Acad. Sci. USA 111 (2014) 6263 - 6268 doi: 10.1073/pnas.1320544111
96.	A. Schwaighofer, M. Pechlaner, C. Oostenbrink, C. Kotlowski, C. Araman, R. Mastrogiacomo, P. Pelosi, W. Knoll, M. Larisika, C. Nowak Insights into structural features determining odorant affinities to honey bee odorant-binding protein 14 Biochem. Biophys. Res. Commun. 446 (2014) 1042–1046 doi: 10.1016/j.bbrc.2014.03.054
95.	Z. Lin, C. Oostenbrink, W.F. van Gunsteren On the use of one-step perturbation to investigate the dependence of NOE derived atom-atom distance bound violations of peptides upon a variation of force-field parameters Eur. Biophys. J. 43 (2014) 113 - 119 doi: 10.1007/s00249-014-0943-3
94.	J.A. Garate, T. Perez-Acle and C. Oostenbrink On the thermodynamics of carbon nanotube single-file water loading: Free energy, Energy and Entropy calculations Phys. Chem. Chem. Phys. 16 (2014) 5119 - 5128 doi: 10.1039/C3CP54554G
93.	B. Lai, C. Hasenhindl, C. Obinger and C. Oostenbrink Molecular dynamics simulation of the crystallizable fragment of IgG1 – Insights for the design of Fcabs Int. J. Mol. Sci. 15 (2014) 438-455 doi:10.3390/ijms15010438
92.	B. Lai, G. Nagy, J.A. Garate and C. Oostenbrink Entropic and enthalpic contributions to stereospecific ligand binding from enhanced sampling methods J. Chem. Inf. Model. 54 (2014) 151 – 158 doi: 10.1021/ci4006657
91.	G. Nagy and C. Oostenbrink Dihedral-based segment identification and classification of biopolymers II: Polynucleotides J. Chem. Inf. Model. 54 (2014) 278 – 288 doi: 10.1021/ci400542n
90.	G. Nagy and C. Oostenbrink Dihedral-based segment identification and classification of biopolymers I: Proteins J. Chem. Inf. Model. 54 (2014) 266 – 277 doi: 10.1021/ci400541d
89.	M.M. Reif and C. Oostenbrink Net charge changes in the calculation of relative ligand-binding free energies via classical atomistic molecular dynamics simulation J. Comput. Chem. 35 (2014) 227–243 doi: 10.1002/jcc.23490
88.	L. Peric-Hassler, E. Stjernschantz, C. Oostenbrink and D.P. Geerke CYP 2D6 binding affinity predictions using multiple ligand and protein conformations Int. J. Mol. Sci. 14 (2013) 24514-24530 doi: 10.3390/ijms141224514
87.	D. Artner, A. Oblak, S. Ittig, J.A. Garate, S. Horvat, C. Arrieumerlou, A. Hofinger, C. Oostenbrink, R. Jerala, P. Kosma and A. Zamyatina Conformationally Constrained Lipid A Mimetics for Exploration of Structural Basis of TLR4/MD-2 Activation by Lipopolysaccharide ACS Chem. Biol. 8 (2013) 2423−2432 doi: 10.1021/cb4003199
86.	C. Zou, M. Larisika, G. Nagy, J. Srajer, C. Oostenbrink, X. Chen, W. Knoll, B. Liedberg, C. Nowak Two-dimensional heterospectral correlation analysis of the redox-induced conformational transition in Cytochrome c using surface-enhanced Raman and infrared absorption spectroscopies on a two-layer gold surface J. Phys. Chem. B 117 (2013) 9606 - 9614 doi: 10.1021/jp404573q
85.	D. Petrov, C. Margreitter, M. Grandits, C. Oostenbrink, B. Zagrovic A Systematic Framework for Molecular Dynamics Simulations of Protein Posttranslational Modifications PLOS Comput. Biol. 9 (2013) e1003154 doi:10.1371/journal.pcbi.1003154
84.	A. Sündermann and C. Oostenbrink Molecular dynamics simulations give insight into the conformational change, complex formation and electron transfer pathway for cytochrome P450 reductase Protein Science 22 (2013) 1183 - 1195 doi: 10.1002/pro.2307
83.	M. M. H. Graf, U. Bren, D. Haltrich and C. Oostenbrink Molecular dynamics simulations give insight into D-glucose dioxidation at C2 and C3 by Agaricus meleagris pyranose dehydrogenase J. Comp-Aided Mol. Des. 27 (2013) 295 - 304 doi: 10.1007/s10822-013-9645-7
82.	M. Grandits, H. Michlmayr, C. Sygmund and C. Oostenbrink Calculation of substrate binding affinities for a bacterial GH78 rhamnosidase through molecular dynamics simulations Mol. Catal. B. 92 (2013) 34-43 doi: 10.1016/j.molcatb.2013.03.012
81.	J.A. Garate and C. Oostenbrink Free energy differences between states with different conformational ensembles J. Comput. Chem. 34 (2013) 1398 - 1408 doi: 10.1002/jcc.23276
80.	A. de Ruiter, S. Boresch and C. Oostenbrink Comparison of thermodynamic integration and Bennett’s acceptance ratio for calculating relative protein – ligand binding free energies J. Comput. Chem 34 (2013) 1024 - 1034 doi: 10.1002/jcc.23229
79.	M.M. Reif, M. Winger and C. Oostenbrink Testing of the GROMOS force-field parameter set 54A8: Structural properties of electrolyte solutions, lipid bilayers and proteins J. Chem. Theory Comput. 9 (2013) 1247 - 1264 DOI: 10.1021/ct300874c
78.	A. de Ruiter and C. Oostenbrink Protein-ligand binding from distancefield distances and Hamiltonian replica exchange simulations J. Chem. Theory Comp. 9 (2013) 883 - 892 doi: 10.1021/ct300967a
77.	J.A. Garate and C. Oostenbrink Lipid A from lipopolysaccharide recognition: Structure, dynamics and cooperativity by molecular dynamics simulation Proteins 81 (2013) 658 - 674 doi: 10.1002/prot.24223
76.	S. Hofbauer, M. Bellei, A. Sündermann, K.F. Pirker, A. Hagmüller, G. Mlynek, J. Kostan, H. Daims, P.G. Furtmüller, K. Djinović-Carugo, C. Oostenbrink, G. Battistuzzi and C.Obinger Redox thermodynamics of high-spin and low-spin forms of chlorite dismutases of diverse subunit and oligomeric structure Biochemistry 51 (2012) 9501 - 9512 doi: 10.1021/bi3013033
75.	G. Nagy and C. Oostenbrink Rationalization of Sterospecific Binding of Propanolol to Cytochrome P450 2D6 by Free Energy Calculations Eur. Biophys. J. 41 (2012) 1065 - 1076 doi: 10.1007/s00249-012-0865-x
74.	M.M. Reif, L. Mach and C. Oostenbrink Molecular insight into propeptide-protein interactions in cathepsins L and O Biochemistry 51 (2012) 8636−8653 doi: 10.1021/bi300802a
73.	B. Lai and C. Oostenbrink Binding free energy, energy and entropy calculations using simple model systems Theor. Chem. Acc.131 (2012) 1272 doi: 10.1007/s00214-012-1272-1
72.	S.B.A. de Beer, H. Venkataraman, D.P. Geerke, C. Oostenbrink and N.P.E. Vermeulen Free energy calculations give insight into the stereoselective hydroxylation of α-ionones by engineered Cytochrome P450 BM3 mutants J.Chem. Inf. Model. 52 (2012) 2139 - 2148 doi: 10.1021/ci300243n
71.	U. Bren and C. Oostenbrink Cytochrome P450 3A4 Inhibition by Ketoconazole: Tackling the Problem of Ligand Cooperativity Using Molecular Dynamics Simulations and Free-Energy Calculations J. Chem. Inf. Model. 52 (2012) 1573 - 1582 doi: 10.1021/ci300118x
70.	M.M. Reif, P. Hünenberger and C. Oostenbrink New interaction parameters for charged amino acid side chains in the GROMOS force field J. of Chem. Theory and Comp. 8 (2012) 3705 - 3723 doi: 10.1021/ct300156h
69.	R. Gößler-Schöfberger, G. Hesser, M.M. Reif, J. Friedmann, B. Duscher, J.L. Toca-Herrera, C. Oostenbrink, A. Jilek A stereochemical switch in the aDrs model system, a candidate for a functional amyloid Arch. Biochem. Biophys. 522 (2012) 100 - 106 doi: 10.1016/j.abb.2012.04.006
68.	D. Steiner, C. Oostenbrink and W.F. van Gunsteren Calculation of the Relative Free Energy of Oxidation of Azurin at pH 5 and pH 9 J. Comput. Chem. 33 (2012) 1467 - 1477 doi: 10.1002/jcc.22972
67.	A. de Ruiter and C. Oostenbrink Efficient and accurate free energy calculations on trypsin inhibitors J. Chem. Theory Comp. 8 (2012) 3686 - 3695 doi: 10.1021/ct200750p
66.	C. Oostenbrink, A. de Ruiter, J. Hritz and N. Vermeulen Malleability and Versatility of Cytochrome P450 Active Sites Studied by Molecular Simulations Current Drug Metabolism, 13 (2012) 190 - 196
65.	C. Oostenbrink „Free energy calculations from one-step perturbations“ in „Methods in Molecular Biology“, “Computational Drug Discovery and Design”, Vol. 819 Humana Press, New York, 487 - 499, (2012)
64.	A.K. Malde, Le Zuo, M. Breeze, M. Stroet, D. Poger, P.C. Nair. C. Oostenbrink, and A.E. Mark An Automated Force Field Topology Builder (ATB) and Repository: Version 1.0 J. Chem. Theory Comp. 7 (2011 ) 4026 – 4037 doi: 10.1021/ct200196m
63.	S. Riniker, C.D. Christ, H.S. Hansen, P.H. Hünenberger, C. Oostenbrink, D. Steiner and W.F. van Gunsteren Calculation of relative free energies for ligand-protein binding, solvation and conformational transitions using the GROMOS software J. Phys. Chem. B 115 (2011) 13570 - 13577 doi: 10.1021/jp204303a
62.	A.P. Eichenberger, J.R. Allison, J. Dolenc, D.P. Geerke, B.A.C. Horta, K. Meier, C. Oostenbrink, N. Schmid, D. Steiner, D. Wang and W.F. van Gunsteren GROMOS++ Software for the Analysis of Biomolecular Simulation Trajectories J. Chem. Theory Comp. 7 (2011) 3379 - 3390 doi: 10.1021/ct2003622
61.	J.H.M. Lange, J. Venhorst, M.J.P. van Dongen, J. Frankena, F. Bassissi, N.M.W.J. de Bruin, C. den Besten, S.B.A. de Beer, C. Oostenbrink, N. Markova and C.G. Kruse Biophysical and physicochemical methods differentiate highly ligand-efficient human D-amino acid oxidase inhibitors Eur. J. Med. Chem. 46 (2011) 4808 - 4819 doi: 10.1016/j.ejmech.2011.04.023
60.	P. Vasanthanathan, J. Lastdrager, C. Oostenbrink, J.N.M. Commandeur, N.P.E. Vermeulen, F.S. Jorgensen, L. Olsen Identification of CYP1A2 ligands by structure-based virtual screening Med. Chem. Commun. 2 (2011) 853 - 859 doi: 10.1039/c1md00087j
59.	A. de Ruiter and C. Oostenbrink Free energy calculations of protein-ligand interactions Curr. Opin. Chem. Biol. 15 (2011) 547 - 552 doi: 10.1016/j.cbpa.2011.05.021
58.	A. de Ruiter, A. Mader, R. Kunert and C. Oostenbrink Molecular simulations to rationalize humanized Ab2/3H6 activity Aust. J. Chem. 64 (2011) 900 - 909
57.	S.B.A. de Beer, A. Glättli, J. Hutzler, N.P.E. Vermeulen and C. Oostenbrink Molecular dynamics simulations and free energy calculations on the enzyme 4-hydroxyphenylpyruvate dioxygenase J. Comput. Chem. 32 (2011) 2160 - 2169
56.	D. Steiner, C. Oostenbrink, F. Diederich, M. Zürcher, W.F. van Gunsteren Calculation of binding free energies of inhibitors to plasmepsin II J. Comput. Chem. 32 (2011) 1801 - 1812
55.	J. Hritz, T. Läppchen, C. Oostenbrink Calculations of binding affinity between C8-substituted GTP analogs and the bacterial cell-division protein FtsZ Eur. Biophys. J. 29 (2010) 1573 - 1580
54.	P. Vasanthanathan, L. Olsen, F.S. Jorgensen, N.P.E. Vermeulen, C. Oostenbrink Computational prediction of binding affinity for CYP1A2-ligand complexes using empirical free energy calculations Drug Metab. Disp. 38 (2010) 1347 - 1354
53.	E. Stjernschantz, and C. Oostenbrink Improved ligand-protein binding affinity predictions using multiple binding modes Biophys. J. 98 (2010) 2682 - 2691
52.	E. Stjernschantz, J. Reinen, W. Meinl, B.J. George, H. Glatt, N.P.E. Vermeulen, C. Oostenbrink Comparison of murine and human estrogen sulfotransferase inhibition in vitro and in silico - implications for differences in activity, subunit dimerization and substrate inhibition Mol. Cell. Endocrinol. 317 (2010) 127 - 140
51.	T. Venäläinen, F. Molnar, C. Oostenbrink, C. Carlberg and M. Peräkylä Molecular mechanism of allosteric communication in the human PPARalpha-RXRalpha heterodimer Proteins 78 (2010) 873 - 887
50.	R. Santos, J. Hritz and C. Oostenbrink The role of water in molecular docking simulations of Cytochrome P450 2D6 J. Chem. Inf. Model 50 (2010) 146 - 154
49.	S.B.A. de Beer, N.P.E. Vermeulen and C. Oostenbrink The role of water molecules in computational drug design Curr. Top. Med. Chem. 10 (2010) 55 - 66
48.	G. Zoldak, T. Aumüller, C. Lücke, J. Hritz, C. Oostenbrink, G. Fischer, F.X. Schmid A library of fluorescent peptides for exploring the substrate specificities of prolyl isomerases Biochemistry 48 (2009) 10423 - 10436
47.	P. Rydberg, P. Vasanthanathan, C. Oostenbrink and L. Olsen Fast prediction of cytochrome P450 mediated drug metabolism ChemMedChem 4 (2009) 2070 - 2079
46.	J. Hritz and C. Oostenbrink Efficient free energy calculations for compounds with multiple stable conformations separated by high energy barriers J. Phys. Chem. B. 113 (2009) 12711 - 12720
45.	P. Vasanthanathan, O. Taboureau, C. Oostenbrink, N.P.E. Vermeulen, L. Olsen and F.S. Jorgensen Classification of Cytochrome P450 1A2 Inhibitors and Non-Inhibitors by Machine Learning Techniques Drug Metab. Disp. 37 (2009) 658 - 664
44.	P. Vasanthanathan, J. Hritz, O. Taboureau, L. Olsen and F.S. Jorgensen, N.P.E. Vermeulen and C. Oostenbrink Virtual screening and prediction of site of metabolism for cytochrome P450 1A2 ligands J. Chem. Inf. Model. 49 (2009) 43 - 52
43.	C. Oostenbrink Efficient free energy calculations on small molecule host-guest systems - a combined Linear Interaction Energy / One-Step perturbation approach J. Comput. Chem. 30 (2009) 212 - 221
42.	J. Hritz, A. de Ruiter and C. Oostenbrink Impact of plasticity and flexibility on docking results for Cytochrome P450 2D6: a combined approach of molecular dynamics and ligand docking J. Med. Chem. 51 (2008) 7469 - 7477
41.	E. Stjernschantz, N.P.E. Vermeulen and C. Oostenbrink Computational prediction of drug binding and rationalisation of selectivity towards Cytochromes P450 Expert Opin. Drug Metab. Toxicol. 4 (2008) 513 - 527
40.	J. Hritz and C. Oostenbrink Hamiltonian replica exchange molecular dynamics using soft-core interactions J. Chem. Phys. 128 (2008) 144121
39.	E. Stjernschantz, B.M.A. van Vugt-Lussenburg, A. Bonifacio, S.B.A. de Beer, G. van der Zwan, C. Gooijer, J.N.M. Commandeur, N.P.E. Vermeulen and C. Oostenbrink Structural rationalization of novel drug metabolizing mutants of cytochrome P450 BM3 Proteins 71 (2008) 336 - 352
38.	J. Hritz and C. Oostenbrink Optimization of replica exchange molecular dynamics by fast mimicking J. Chem. Phys. 127 (2007) 204104
37.	W.F. van Gunsteren, D.P. Geerke, D. Trzesniak, C. Oostenbrink and N.F.A. van der Vegt Analysis of the driving forces for biomolecular solvation and association Proc. Italian School of Physics "Enrico Fermi", Course CLXV, R.A. Broglia, L. Serrano and G. Tiana (Eds.), IOS Press, Amsterdam - SIF, Bologna (2007) 177 - 191
36.	C. de Graaf, C. Oostenbrink, P.H.J. Keizers, B.M.A. van Vugt-Lussenburg, J.N.M. Commandeur, N.P.E. Vermeulen Free energies of binding of R- and S-propranolol to wildtype and F483A mutant Cytochrome P450 2D6 from molecular dynamics simulations Eur. Biophys. J. 36 (2007) 589 - 599
35.	C. Oostenbrink, M.M.H. van Lipzig and W.F. van Gunsteren Applications of molecular dynamics simulations in drug design In: "Comprehensive Medicinal Chemistry II" Vol. 4, Computer-Assisted Drug Design, J.B. Taylor and D.J. Triggle Eds., Elsevier, Amsterdam, 2007, pp 651-668
34.	B.M.A. van Vugt-Lussenburg, E. Stjernschantz, J. Lastdrager, C. Oostenbrink, N.P.E. Vermeulen and J.N.M. Commandeur Identification of novel critical residues in drug metabolising mutants of Cytochrome P450 BM3 using random mutagenesis J. Med. Chem. 50 (2007) 455 - 461
33.	B. Keller, M. Christen, C. Oostenbrink, W.F. van Gunsteren On using oscillating time-dependent restraints in MD simulation J. Biomol. NMR 37 (2007) 1 - 14
32.	C. de Graaf, C. Oostenbrink, P. Keizers, B. van Vugt-Lussenburg, R. van Waterschoot, R. Tschirret-Guth, J. Commandeur, N.P.E. Vermeulen Molecular modeling-guided site-directed mutagenesis of cytochrome P450 2D6 Curr. Drug. Metab. 8 (2007) 59 - 77
31.	E. Stjernschantz, J. Marelius, C. Medina, M. Jacobsson, N.P.E. Vermeulen and Chris Oostenbrink Are automated molecular dynamics simulations and binding free energy calculations realistic tools in lead optimization? - An evaluation of the linear interaction energy (LIE) method J. Chem. Inf. Model. 46 (2006) 1972 - 1983
30.	J. Dolenc, R. Baron, C. Oostenbrink, J. Koller and W.F. van Gunsteren Configurational entropy change of netropsin and distamycin upon DNA minor-groove binding Biophys. J. 91 (2006) 1460 - 1470
29.	W.F. van Gunsteren, D. Bakowies, R. Baron, I. Chandrasekhar, M. Christen, X. Daura, P.Gee, D.P. Geerke, A. Glättli, P.H. Hünenberger, M.A. Kastenholz, C. Oostenbrink, M. Schenk, D. Trzesniak, N.F.A. van der Vegt and H.B. Yu Biomolecular modeling: goals, problems, perspectives Angew. Chem 118 (2006) 4168-4198 Angew. Chem. Int. Ed. 45 (2006) 4064-4092
28.	C. de Graaf, C. Oostenbrink, P.H.J. Keizers, T. van der Wijst, A. Jongejan, N.P.E. Vermeulen Catalytic site prediction and virtual screening of cytochrome P450 2D6 substrates by consideration of water and rescoring in automated docking J. Med. Chem. 49 (2006) 2417 - 2430
27.	Y. Zhou, C. Oostenbrink, A. Jongejan, W.F. van Gunsteren, W.R. Hagen, S.W. de Leeuw, J.A. Jongejan Computational study of ground state chiral induction in small peptides: Comparison of the relative stability of selected amino acid dimers and oligomers in homochiral and heterochiral combinations J. Comput. Chem. 27 (2006) 857-867
26.	C. Oostenbrink and W.F. van Gunsteren Calculating zeros: non-equilibrium free energy calculations Chem. Phys. 323 (2006) 102-108
25.	A. Stortelder, P.H.J. Keizers, C. Oostenbrink, C. de Graaf, P. de Kruijf, N.P.E. Vermeulen, C. Gooijer, J.N.M. Commandeur, G. van der Zwan Binding of 7-methoxy-4-(aminomethyl)-coumarin to wild-type and W128F mutant cytochrome P450 2D6 studied by time-resolved fluorescence spectroscopy Biochem. J., 393 (2006) 635 - 643
24.	M. Christen, D. Bakowies, R. Baron, R. Bürgi, D. Geerke, T. Heinz, P. Hünenberger, M. Kastenholz, V. Kräutler, C. Oostenbrink, C. Peter, D. Trzesniak and W.F. van Gunsteren The GROMOS software for biomolecular simulation: GROMOS05 J. Comput. Chem., 26 (2005) 1719 - 1751
23.	C. Oostenbrink, D. Juchli, W.F. van Gunsteren Amine hydration: A united-atom force field solution Chem. Phys. Chem., 6 (2005) 1800 - 1804
22.	P.H.J. Keizers, C. de Graaf, F.J.J. de Kanter, C. Oostenbrink, K.A. Feenstra, J.N.M. Commandeur and N.P.E. Vermeulen Metabolic regio- and stereoselectivity of cytochrome P450 2D6 towarSubmitted to J.Chem. Inf. Model. (2012)ds 3,4-methylenedioxy-N-alkylamphetamines: in silico predictions and experimental validation J. Med. Chem., 48 (2005) 6117 - 6127
21.	C. Oostenbrink and W.F. van Gunsteren Efficient calculation of stacking and pairing free energies in DNA from molecular dynamics simulations Chem. Eur. J., 11 (2005) 4340 - 4348
20.	Y. Zhou, C. Oostenbrink, W.F. van Gunsteren, W.R. Hagen, S.R. de Leeuw, J. Jongejan Relative stability of homochiral and heterochiral dialanine peptides. Effects of perturbation pathways and force-field parameters on free energy calculations Mol. Phys., 104 (2005) 1961 - 1969
19.	C. Oostenbrink, T.A. Soares, N.F.A. van der Vegt and W.F. van Gunsteren Validation of the 53A6 GROMOS force field Eur. Biophys. J., 34 (2005) 273 - 284
18.	C. Oostenbrink and W.F. van Gunsteren Free energies of ligand binding for structurally diverse compounds Proc. Natl. Acad. Sci. USA, 102 (2005) 6750 - 6754
17.	M. van den Bosch, M. Swart, J. Snijders, H.J.C. Berendsen, A.E. Mark, C. Oostenbrink, W.F. van Gunsteren and G.W. Canters Calculation of the redox potential of the protein azurin and some mutants ChemBioChem, 6 (2005) 738 - 746
16.	T.A. Soares, P.H. Hünenberger, M.A. Kastenholz, V. Kräutler, T. Lenz, R.D. Lins, C. Oostenbrink and W.F. van Gunsteren An improved nucleic-acid parameter set for the GROMOS force field J. Comput. Chem., 26 (2005) 725 - 737
15.	J. Dolenc, C. Oostenbrink, J. Koller, W.F. van Gunsteren Relative free energies of binding of Netropsin and Distamycin A to DNA Nucl. Acid Res., 33 (2005) 725 - 733
14.	T.A. Soares, X. Daura, C. Oostenbrink, L.J. Smith, W.F. van Gunsteren Validation of the GROMOS Force-field Parameter Set 45A3 against Nuclear Magnetic Resonance Data of Hen Egg Lysozyme J. Biomol. NMR, 30 (2004) 407 - 422
13.	C. Oostenbrink and W.F. van Gunsteren Methane clustering in explicit water: Effect of urea on hydrophobic interactions Phys. Chem. Chem. Phys. 7 (2005) 53 - 58
12.	C. Oostenbrink, A. Villa, A.E. Mark and W.F. van Gunsteren A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6 J. Comp. Chem. 25 (2004) 1656 - 1676
11.	I. Chandrasekhar, C. Oostenbrink and W.F. van Gunsteren Simulating the Physiological Phase of Hydrated Dipalmitoylphosphatidylcholine Bilayers: The Ester Moiety Soft Materials 2 (2004) 27 - 45
10.	A. Glättli, C. Oostenbrink, X. Daura, D.P. Geerke, H. Yu, W.F. van Gunsteren On the transferability of the SPC/L water model to biomolecular simulation Brazilian J. of Phys. 34 (2004) 116-125
9.	C. Peter, C. Oostenbrink, A. van Dorp, W.F. van Gunsteren Estimating entropies from molecular dynamics simulations J. Chem. Phys. 120 (2004) 2652-2661
8.	D.P. Geerke, C. Oostenbrink, N.F.A. van der Vegt and W.F. van Gunsteren An Effective Force Field for Molecular Dynamics Simulations of Dimethyl Sulfoxide and Dimethyl Sulfoxide-Water Mixtures J. Phys. Chem. B 108 (2004) 1436 - 1445
7.	C. Oostenbrink and W.F. van Gunsteren Free energies of binding of polychlorinated biphenyls to the estrogen receptor from a single simulation Proteins 54 (2004) 234-246
6.	C. Oostenbrink and W.F. van Gunsteren Single-step perturbations to calculate free energy differences from unphysical reference states: limits on size, flexibility and character J. Comput. Chem. 24 (2003) 1730-1739
5.	I. Chandrasekhar, M. Kastenholz, R.D. lins, C. Oostenbrink, L.D. Schuler, D.P. Tieleman and W.F. van Gunsteren A consistent potential energy parameter set for lipids: Dipalmitoylphosphatidylcholine as a benchmark of the GROMOS96 45A3 force field Europ. Biophys. J. 32 (2003) 67-77
4.	T. Hansson, C. Oostenbrink and W.F. van Gunsteren Molecular Dynamics Simulations Curr. Opinion Struct. Biol. 12 (2002) 190-196
3.	V.P. Osinga, B.C. Oostenbrink, E. van Lenthe, C. Fonseca Guerra, E.J. Baerends A least squares multicenter approach to continuum wave functions Chem. Phys. 284 (2002) 565 - 574
2.	W.F. van Gunsteren, D. Bakowies, R. Bürgi, I. Chandrasekhar, M. Christen, X. Daura, P. Gee, A. Glättli, T. Hansson, C. Oostenbrink, C. Peter, J. Pitera, L. Schuler, T. Soares and H. Yu Molecular Dynamics Simulation of Biomolecular Systems CHIMIA 55 (2001) 856-860
1.	B.C. Oostenbrink, J.W. Pitera, M.M.H. van Lipzig, J.H.N. Meerman and W.F. van Gunsteren Simulations of the Estrogen Receptor Ligand Binding Domain: the affinity of natural ligands and xenoestrogens J. Med. Chem. 43 (2000) 4594-4605

Publications in Print

published

a.		A. de Ruiter and C. Oostenbrink Binding free energy calculations in drug discovery Submitted as book chapter in Computational drug discovery: methods and applications, ed. P. Vasanthanathan (2022)
b.		C. Stefanović, F.F. Hager-Mair, E. Breslmayr, A. López Guzmán, C. Lim, M. Blaukopf, P. Kosma, C. Oostenbrink, R. Ludwig, and C. Schäffer Molecular modelling and site-directed mutagenesis provide insight into saccharide pyruvylation by the Paenibacillus alvei CsaB enzyme Submitted to Sci. Rep. (2023)
c.		P. Maleš, Z. Brkljača, I. Crnolatac, D. Petrov and D. Bakarić Lysine Residues are Crucial for the Phase-Dependent Adhesion of Myelin Basic Protein to Phosphatidylcholine Lipid Bilayers Submitted to Langmuir (2023)
d.		D. Petrov, J.W. Perthold, C. Oostenbrink, B.L. de Groot and V. Gapsys Guidelines for free energy calculations involving charge changes Submitted to J. Chem. Theory Comput. (2023)
e.		M. Zemkollari, C. Oostenbrink, R. Grabherr and E. Staudacher Molecular cloning, characterisation and molecular modelling of two novel T-synthases from mollusc origin Submitted to J. Biol. Chem. (2023)
f.		E. Hermann, C.F. Rodrigues, L.O. Martins, C. Peterbauer, and C. Oostenbrink, Engineering A-type Dye-decolorizing Peroxidases by Modification of a Conserved Glutamate Residue Submitted to Biochemistry (2023)
g.		M. Broz, C. Oostenbrink and U. Bren The Effect of Microwaves on Protein Structure: Molecular Dynamics Approach Submitted to J. Chem. Theory Comput. (2023)
h.		J. Stöckelmaier and C. Oostenbrink Conformational Dependence of Chemical Shifts in the Proline Rich Region of TAU Protein Submitted to J. Chem. Theory Comput. (2023)

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Publications

Publications in Print