in Druck

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 <hr /
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
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/

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/

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/


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/
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/

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/

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. E. 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
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
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
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/


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/


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/


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/


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/



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/



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/


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/


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/


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/


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/


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/


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/


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/


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/


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/


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/


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/


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/


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/


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/


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/


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/


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/


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/


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/


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/


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/


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/


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/


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/


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/


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


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)


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/


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/


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/


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/


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/


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/


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


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


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


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


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


E. Stjernschantz, and C. Oostenbrink
Improved ligand-protein binding affinity predictions using multiple binding modes
Biophys. J. 98 (2010) 2682 - 2691


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


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


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


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


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


P. Rydberg, P. Vasanthanathan, C. Oostenbrink and L. Olsen
Fast prediction of cytochrome P450 mediated drug metabolism
ChemMedChem 4 (2009) 2070 - 2079


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


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


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


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


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


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


J. Hritz and C. Oostenbrink
Hamiltonian replica exchange molecular dynamics using soft-core interactions
J. Chem. Phys. 128 (2008) 144121


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


J. Hritz and C. Oostenbrink
Optimization of replica exchange molecular dynamics by fast mimicking
J. Chem. Phys. 127 (2007) 204104


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


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


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


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


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


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


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


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


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


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


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


C. Oostenbrink and W.F. van Gunsteren
Calculating zeros: non-equilibrium free energy calculations
Chem. Phys. 323 (2006) 102-108


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


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


C. Oostenbrink, D. Juchli, W.F. van Gunsteren
Amine hydration: A united-atom force field solution
Chem. Phys. Chem., 6 (2005) 1800 - 1804


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


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


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


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


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


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


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


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


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


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


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


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


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


C. Peter, C. Oostenbrink, A. van Dorp, W.F. van Gunsteren
Estimating entropies from molecular dynamics simulations
J. Chem. Phys. 120 (2004) 2652-2661


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


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


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


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


T. Hansson, C. Oostenbrink and W.F. van Gunsteren
Molecular Dynamics Simulations
Curr. Opinion Struct. Biol. 12 (2002) 190-196


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


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


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

Publikationen in Druck


a.   V. Monteil, S. Devignot, J. Klingström, C. Thålin, M.J. Kellner, W. Christ, S. Havervall, S. Mereiter, S. Knapp, N. Montserrat, B. Braunsfeld, I. Kozieradzki, O. Hasan Ali, A. Hagelkruys, J. Stadlmann, C. Oostenbrink, G. Wirnsberger, J.M. Penninger, and A. Mirazimi
Clinical grade ACE2 effectively inhibits SARS-CoV-2 Omicron 1 infections
Submitted to Nat. Biotech. (2021)
doi: 10.1101/2021.12.25.474113
b.   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)
c.   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
Submitted to ACS Infectious Diseases (2022)
d.   E. Galicia-Andrés, Y. Escalona, M. Gotsmy, C. Oostenbrink and D. Petrov
Molecular Dynamics Simulations up to Earth: Modeling of Soil Organic Matter
Submitted to Comprehensive Computational Chemistry (2023)
e.   O. Gracia Carmona, M. Gillhofer, L. Tomasiak, A. de Ruiter, C. Oostenbrink
Accelerated enveloping distribution sampling to probe the presence of water molecules
Submitted to J. Chem. Theory Comput. (2023)
f.   Y. Escalona, D. Petrov, E. Galicia-Andrés and C. Oostenbrink
Exploring the Macroscopic Properties of Humic Substances using Modeling and Molecular Simulations
Submitted to Agronomy (2023)
g.   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)