246. | T. Kuvek, C. Marcher, A. Berteotti, V. Lopez Carrillo, K.J. Schleifer and C. Oostenbrink A computational pipeline observes the flexibility and dynamics of plant cytochrome P450 binding sites Int. J. Mol. Sci. 25 (2024) 11381 doi: 10.3390/ijms252111381
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245. | X. Liu, A. Ortega-Guerrero, N.P. Domingues, M.J. Pougin, B. Smit, L. Hosta-Rigau and C. Oostenbrink Stability assessment in aqueous and organic solvents of metal-organic framework PCN 333 nanoparticles through a combination of physicochemical characterization and computational simulations Langmuir (2024), online doi: 10.1021/acs.langmuir.4c01684
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244. | M. Borisover, D. Petrov, C. Oostenbrink, E. Galicia-Andrés Diluting humic substances in water in molecular dynamics simulations: Are aggregates stable? Colloids and Surfaces A, 704 (2025) 135507 doi: 10.1016/j.colsurfa.2024.135507
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243. | A. de Ruiter and C. Oostenbrink Binding free energy calculations in drug discovery in "Computational drug discovery: methods and applications", Wiley, Weinheim, pages 3 - 20 (2024) doi: 10.1002/9783527840748
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242. | C. Stefanović, M.S. Legg, N. Mateyko, J. Ender, T. Kuvek, C. Oostenbrink, C. Schäffer, S.V. Evans, F.F. Hager-Mair Insights into structure and activity of a UDP-GlcNAc 2-epimerase involved in secondary cell wall polymer biosynthesis in Paenibacillus alvei Front. Mol. Biosci. 11 (2024) 1470989, online doi: 10.3389/fmolb.2024.1470989
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241. | J. Stöckelmaier and C. Oostenbrink Conformational Dependence of Chemical Shifts in the Proline Rich Region of TAU Protein Phys. Chem. Chem. Phys. 26, 2024, 23856 – 23870 doi: 10.1039/D4CP02484B
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240. | W.F. van Gunsteren and C. Oostenbrink Methods for Classical-Mechanical Molecular Simulation in Chemistry: Achievements, Limitations, Perspectives J. Chem. Inf. Model. (2024), online doi: 10.1021/acs.jcim.4c00823
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239. | H. Verli and C. Oostenbrink Status and prospects of molecular simulations for drug discovery J. Brazil. Chem. Soc. 35 (2024), e-20240119, 1-15 doi: 10.21577/0103-5053.20240119
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238. | J.D.H. Liu, A. Fischer, M. Cserjan-Puschmann, N. Lingg, C. Oostenbrink Caspase-Based Fusion Protein Technology: Substrate Cleavability Described by Computational Modeling and Simulation J. Chem. Inf. Model. (2024) online doi: 10.1021/acs.jcim.4c00316
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237. | M. Stroet, M. Setz, T. Lee, A.K. Malde, G. van den Bergen, P. Sykacek, C. Oostenbrink and A.E. Mark On the validation of protein force fields based on structural criteria. J. Phys. Chem. B (2024), online doi: 10.1021/acs.jpcb.3c08469
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236. | M. Broz, C. Oostenbrink and U. Bren The Effect of Microwaves on Protein Structure: Molecular Dynamics Approach J. Chem. Inf. Model. (2024), online doi: 10.1021/acs.jcim.3c01937
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235. | 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 ChemBioChem (2024), e202300872 doi: 10.1002/cbic.202300872
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234. | M. Zemkollari, C. Oostenbrink, R. Grabherr and E. Staudacher Molecular cloning, characterisation and molecular modelling of two novel T-synthases from mollusc origin Glycobiology 34 (2024), cwae013 doi: 10.1093/glycob/cwae013
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233. | P. Maleš, Z. Brkljača, I. Crnolatac, D.Petrov and D. Bakarić Phase-Dependent Adsorption of Myelin Basic Protein to Phosphatidylcholine Lipid Bilayers Membranes 14, (2024) 15 doi: 10.3390/membranes14010015
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232. | D. Petrov, J.W. Perthold, C. Oostenbrink, B.L. de Groot and V. Gapsys Guidelines for free energy calculations involving charge changes J. Chem. Theory Comput. (2024) online doi: 10.1021/acs.jctc.3c00757
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231. | 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 Sci. Rep. 13, (2023) 13394 doi: 10.1038/s41598-023-40072-1
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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) e3068 doi: 10.1002/jmr.3068
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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. 63 (2023), 6642 - 6654 doi: 10.1021/acs.jcim.3c00418
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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 24 (2023), e202300431 doi: 10.1002/cbic.202300431
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227. | O. Gracia Carmona and C. Oostenbrink Flexible Gaussian accelerated molecular dynamics to enhance biological sampling J. Chem. Theory Comput. 19 (2023) 6521 – 6531 doi: 10.1021/acs.jctc.3c00619
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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
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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. 19 (2023) 3379 – 3390 doi: 10.1021/acs.jctc.3c00109
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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. 63 (2023) 2495 – 2504 doi: 10.1021/acs.jcim.3c00173
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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
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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. 63 (2023) 197–207 doi: 10.1021/acs.jcim.2c01272
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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
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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
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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
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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
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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 61 (2022) 2049 – 2062 doi: 10.1021/acs.biochem.2c00384
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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
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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
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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. 14 (2022) e15230 doi: 10.15252/emmm.202115230
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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166. | M. Maurer and C. Oostenbrink Water in Protein Hydration and Ligand Recognition J. Mol. Recogn. 32 (2019), e2810 doi: 10.1002/jmr.2810
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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113. | M. Grandits, A. Sündermann and C. Oostenbrink LUCI4HPC Linux Journal 252 (2015), 68 - 76
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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91.
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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)
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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53.
| E. Stjernschantz, and C. Oostenbrink Improved ligand-protein binding affinity predictions using multiple binding modes Biophys. J. 98 (2010) 2682 - 2691
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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
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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
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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
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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
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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
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47.
| P. Rydberg, P. Vasanthanathan, C. Oostenbrink and L. Olsen Fast prediction of cytochrome P450 mediated drug metabolism ChemMedChem 4 (2009) 2070 - 2079
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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
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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
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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
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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
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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
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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
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40.
| J. Hritz and C. Oostenbrink Hamiltonian replica exchange molecular dynamics using soft-core interactions J. Chem. Phys. 128 (2008) 144121
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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
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38.
| J. Hritz and C. Oostenbrink Optimization of replica exchange molecular dynamics by fast mimicking J. Chem. Phys. 127 (2007) 204104
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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26.
| C. Oostenbrink and W.F. van Gunsteren Calculating zeros: non-equilibrium free energy calculations Chem. Phys. 323 (2006) 102-108
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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
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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
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23.
| C. Oostenbrink, D. Juchli, W.F. van Gunsteren Amine hydration: A united-atom force field solution Chem. Phys. Chem., 6 (2005) 1800 - 1804
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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4.
| T. Hansson, C. Oostenbrink and W.F. van Gunsteren Molecular Dynamics Simulations Curr. Opinion Struct. Biol. 12 (2002) 190-196
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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
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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
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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
| |