Publikationen


Publikationen

in Druck

139.A. Turupcu and C. Oostenbrink
Modeling of oligosaccharides within glycoproteins from free-energy landscapes
J. Chem. Inf. Model. (2017) online
doi: 10.1021/acs.jcim.7b00351
138.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
137.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., Online (2017)
doi: 10.1002/anie.201702945
doi:
10.1002/ange.201702945
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 Sensors, (2017) online
doi: 10.1021/acssensors.7b00131

135.L. Montero-Morales, D. Maresch, A. Castilho, A. Turupcu, K. Ilieva, S. Crescioli, S. Karagiannis, C. Lupinek, C. Oostenbrink, F. Altmann, H. Steinkellner
Recombinant plant-derived human IgE glycoproteomics
J. Proteom. 161 (2017) 81 - 87
doi: 10.1016/j.jprot.2017.04.002
134.D. Petrov, D. Tunega, M.H. Gerzabek, C. Oostenbrink
Molecular dynamics simulations of the standard Leonardite humic acid: microscopic analysis of the structure and dynamics
Env. Sci. Techn. 51 (2017) 5414 - 5424
doi: 10.1021/acs.est.7b00266

133.C. Margreitter and C. Oostenbrink
MDplot: Visualise Molecular Dynamics
The R Journal 9 (2017), 164 - 186
https://journal.r-project.org/archive/2017/RJ-2017-007/index.html

132.I. Grishkovskaya, M. Paumann-Page, R. Tscheliessnig, J.a Stampler, S.Hofbauer, M. Soudi, B. Sevcnikar, C. Oostenbrink, P.G. Furtmüller, K. Djinović-Carugo, W.M. Nauseef and C. Obinger
Structure of human promyeloperoxidase (proMPO) and the role of the propeptide for processing and maturation
J. Biol. Chem.,  292 (2017) 8244 - 8261
doi: 10.1074/jbc.M117.775031

131.C. Margreitter, M.M. Reif and C. Oostenbrink
Update on phosphate and charged post-translationally modified amino acid parameters in the GROMOS force field
J. Comput. Chem. 38 (2017) 714 – 720
doi: 10.1002/jcc.24733
130.M. Pechlaner, M. Reif, C. Oostenbrink
Reparametrization of United-Atom Amine Solvation in the GROMOS Force Field
Mol. Phys. 115 (2017) 1144 - 1154
doi: 10.1080/00268976.2016.1255797

129.W. F. van Gunsteren, J. R. Allison, X. Daura, J. Dolenc, N. Hansen, A.E. Mark, C. Oostenbrink, V. H. Rusu, L. J. Smith
Deriving structural information from experimentally measured data on biomolecules
Angew. Chem. 128 (2016) 16222 – 16244
doi:10.1002/ange.201601828
Angew. Chem. Int. Ed. 55 (2016) 15990 – 16010
doi: 10.1002/anie.201601828

128.J. van Leeuwen, C. Pons, J.C. Mellor, T.N. Yamaguchi, H. Friesen, J. Koschwanez, M. Mattiazzi Ušaj, M. Pechlaner, M. Takar, M. Ušaj, B. VanderSluis, K. Andrusiak, P. Bansal, A. Baryshnikova, C. Boone, J. Cao, A. Cote, M. Gebbia, G. Horecka, I. Horecka, E. Kuzmin, N. Legro, W. Liang, N. van Lieshout, M. McNee, B.-J. San Luis, F. Shaeri, E. Shuteriqi, S. Sun, L. Yang, J.-Y. Youn, M. Yuen, M. Costanzo, A.-C. Gingras, P. Aloy, C. Oostenbrink, A. Murray, T.R. Graham, C.L. Myers, B.J. Andrews, F.P. Roth, and C. Boone
Exploring Genetic Suppression Interactions on a Global Scale
Science 354 (2016), aag0839
doi: 10.1126/science.aag0839

127.M.M.H. Graf, M. Maurer, and C. Oostenbrink
Free-energy calculations of residue mutations in a tripeptide using various methods to overcome inefficient sampling
J. Comput. Chem. 37 (2016), 2597 - 2605
doi: 10.1002/jcc.24488

126.S. Hofbauer, M. Dalla Sega, S. Scheiblbrandner, Z. Jandova, I. Schaffner, G. Mlynek, K. Djinovic-Carugo, G. Battistuzzi, P.G. Furtmüller, C. Oostenbrink, C. Obinger
Chemistry and molecular dynamics simulations of heme b-HemQ and coproheme-HemQ
Biochemistry 55 (2016), 5398–5412
doi: 10.1021/acs.biochem.6b00701

125.C. Margreitter and C. Oostenbrink
On the optimization of the protein backbone dihedral angles by means of Hamiltonian reweighting
J. Chem. Inf. Model. 56 (2016) 1823 - 1834
doi: 10.1021/acs.jcim.6b00399

124.A. de Ruiter and C. Oostenbrink
Extended Thermodynamic Integration: efficient prediction of lambda derivatives at non-simulated points
J. Chem. Theory Comput. 12 (2016) 4476 - 4486
doi: 10.1021/acs.jctc.6b00458

123.B. Gasselhuber, M.M.H. Graf, C. Jakopitsch, M. Zamocky, A. Nicolussi, P.G. Furtmüller, C. Oostenbrink, X. Carpena and C. Obinger
Interaction with the redox cofactor MYW and functional role of a mobile arginine in eukaryotic catalase-peroxidase
Biochemistry 55 (2016), 3528 - 3541
doi: 10.1021/acs.biochem.6b00436

122.M. Maurer, S.B.A. de Beer and C. Oostenbrink
Calculation of relative binding free energy in the water-filled active site of oligopeptide-binding protein A
Molecules 21 (2016), 499
doi: 10.3390/molecules21040499
121.C. Margreitter, P. Mayrhofer, R. Kunert and C. Oostenbrink
Antibody humanization by molecular dynamics simulations – in-silico guided selection of critical backmutations
J. Mol. Recogn. 29 (2016) 266 - 275
doi: 10.1002/jmr.2527

120.L. Olsen, F.S. Jørgensen and C. Oostenbrink
Cytochrome P450 Mediated Drug Metabolism
In "New Horizons in Predictive Drug Metabolism and Pharmacokinetics", Ed. A.G.E. Wilson, Royal Society of Chemistry, Cambridge (2016), pp. 66 - 78
doi: 10.1039/9781782622376-00066

119.M. Pechlaner and C. Oostenbrink
Multiple binding poses in the hydrophobic cavity of bee odorant binding protein AmelOBP14
J. Chem. Inf. Model 55 (2015) 2633 - 2643
doi: 10.1021/acs.jcim.5b00673
118.A. Sündermann, R. Solc, D. Tunega, G. Haberhauer, M.H. Gerzabek, C. Oostenbrink
Vienna Soil Organic Matter Modeler - Generating condensed-phase models of humic substances
J. Mol. Graph. Model. 62 (2015) 243 - 261
doi: 10.1016/j.jmgm.2015.10.007

117.B. Gasselhuber, X. Carpena, M.M.H. Graf, K.F. Pirker, A. Nicolussi, A. Sündermann, S. Hofbauer, M. Zamocky, P.G. Furtmüller, C. Jakopitsch, C. Oostenbrink, I. Fita and C. Obinger
Eukaryotic catalase-peroxidase: the role of the Trp-Tyr-Met adduct in protein stability, substrate accessibility and catalysis of hydrogen peroxide dismutation
Biochemistry 54 (2015) 5425 - 5438
doi: 10.1021/acs.biochem.5b00831
116.M. Graf, J. Sucharitakul, U. Bren, B. Chu, G. Köllensberger, S. Hann, P. Furtmüller, C. Obinger, C. Peterbauer, C. Oostenbrink, P. Chaiyen, D. Haltrich
Reaction of pyranose dehydrogenase from Agaricus meleagris with its carbohydrate substrates
FEBS Journal 282 (2015) 4218 – 4241
doi: 10.1111/febs.13417
115.L. Olsen, C. Oostenbrink, F.S. Jørgensen
Prediction of cytochrome P450 mediated metabolism
Adv. Drug Deliv. Rev. 86 (2015) 61 - 71
doi: 10.1016/j.addr.2015.04.020

114.A. Castilho, C. Gruber, A. Thader, C. Oostenbrink, M. Pechlaner, H. Steinkellner, F. Altmann
Processing of complex N-glycans in IgG Fc-region is affected by core-fucosylation
mAbs 7 (2015), 863 - 870
doi: 10.1080/19420862.2015.1053683
113.M. Grandits, A. Sündermann and C. Oostenbrink
LUCI4HPC
Linux Journal 252 (2015), 68 - 76

112.M. Grandits and C. Oostenbrink
Selectivity of cytosolic phospholipase A2 type IV towards arachidonyl phospholipids
J. Mol. Recogn., 28 (2015) 447 - 457
doi: 10.1002/jmr.2462

111.B. Zolghadr, B. Gasselhuber, M. Windwarder, M. Pabst, D. Kracher, M. Kerndl, S. Zayni, A. Hofinger-Horvath, R. Ludwig, D. Haltrich, C. Oostenbrink, C. Obinger, P. Kosma, P. Messner, and C. Schäffer
UDP-Sulfoquinovose Formation by Sulfolobus acidocaldarius
Extremophiles 19 (2015) 451 - 467
doi: 10.1007/s00792-015-0730-9

110.M.M. Reif and C. Oostenbrink
Towards the correction of effective electrostatic forces in explicit-solvent molecular dynamics simulations: Restraints on solvent-generated electrostatic potential and solvent polarization
Theor. Chem. Acc. 134 (2015) 2
doi: 10.1007/s00214-014-1600-8

109.J.A. Garate, J. Stöckl, M. del Carmen Fernández-Alonso, D. Artner, M. Haegman, C. Oostenbrink, J. Jiménez-Barbero, R. Beyaert, H. Heine, P. Kosma, and A. Zamyatina
Anti-endotoxic Activity and Structural basis for human MD-2·TLR4 Antagonism of Tetraacylated Lipid A Mimetics based on beta-GlcN(1↔1)alpha-GlcN Scaffold
Innate Immun. 21 (2015) 490 - 503
doi: 10.1177/1753425914550426
108.M. M. H. Graf, Z. Lin, U. Bren, D. Haltrich, W. F. van Gunsteren, and C. Oostenbrink
Pyranose Dehydrogenase Ligand Promiscuity: A Generalized Approach to Simulate Monosaccharide Solvation, Binding, and Product Formation
PLOS Comput. Biol. 10 (2014) e1003995
doi: 10.1371/journal.pcbi.1003995

107.A.B. Nørholm, P. Francotte, E. Goffin, I. Botez, L. Danober, P. Lestage, B. Pirotte, J.S. Kastrup, L. Olsen, and C. Oostenbrink
Thermodynamic characterization of new positive allosteric modulators binding to the glutamate receptor A2 ligand-binding domain: combining experimental and computational methods unravels differences in driving forces
J. Chem. Inf. Model 54 (2014) 3404−3416
doi: 10.1021/ci500559b

106.U. Bren, J.E. Fuchs and C. Oostenbrink
Cooperative Binding of Aflatoxin B1 by Cytochrome P450 3A4: A Computational Study
Chem. Res. Toxicol. 27 (2014) 2136−2147
doi: 10.1021/tx5004062

105.M.M. Reif and C. Oostenbrink
Molecular dynamics simulation of configurational ensembles compatible with experimental FRET efficiency data through a restraint on instantaneous FRET efficiencies
J. Comput. Chem. 35 (2014) 2319 - 2332
doi: 10.1002/jcc.23756

104.C.Oostenbrink
Structure-based methods for predicting the sites and products of metabolism
In "Drug Metabolism Prediction", Ed. J. Kirchmair, Wiley, Weinheim (2014), pp. 243 - 263

103.M. Grandits and C. Oostenbrink
Molecular dynamics simulations of the Auxin Binding Protein 1 in complex with indole-3-acetic acid and naphthalen-1-acetic acid
Proteins 82 (2014) 2744 - 2755
doi: 10.1002/prot.24639

102.A. Sündermann, M.M. Reif, S. Hofbauer, C. Obinger and C. Oostenbrink
Investigation of ion binding in chlorite dismutases by means of molecular dynamics simulations
Biochemistry 53 (2014) 4869 - 4879
doi: 10.1021/bi500467h
101.M.W. Traxlmayr, E. Lobner, C. Hasenhindl, G.  Stadlmayr, C. Oostenbrink, F. Rüker and C.  Obinger
Construction of pH-sensitive Her2-binding IgG1-Fc by directed evolution
Biotechnol. J. 9 (2014) 1013 - 1022
doi: 10.1002/biot.201300483

100.E. Németh, G.K. Schilli, G. Nagy, C. Hasenhindl, B. Gyurcsik, C. Oostenbrink
Design of a colicin E7 based chimeric zinc-finger nuclease
J. Comp.-Aided Mol. Des. 28 (2014) 841 - 850
doi: 10.1007/s10822-014-9765-8

99.C. Hasenhindl, B. Lai, J. Delgado, M. W. Traxlmayr, G. Stadlmayr, F. Rüker, L. Serrano, C. Oostenbrink, C. Obinger
Creating stable stem regions for loop elongation in Fcabs – Insights from combining yeast surface display, in silico loop reconstruction and molecular dynamics simulations
Biochim. Biophys. Acta 1844 (2014) 1530 - 1540
doi: 10.1016/j.bbapap.2014.04.020

98.S. Hofbauer, C. Gruber, K.F. Pirker, A. Sündermann, I. Schaffner, C. Jakopitsch, C. Oostenbrink, P.G. Furtmüller, C. Obinger
Transiently produced hypochlorite is responsible for the irreversible inhibition of chlorite dismutase
Biochemistry 53 (2014) 3145 - 3157
doi: 10.1021/bi500401k

97.

A. Loos, C. Gruber, F. Altmann, U. Mehofer, F. Hensel, M. Grandits, C. Oostenbrink, G. Stadlmayr, P.G. Furtmüller, and H. Steinkellner
Expression and glycoengineering of functionally active hetero-multimeric IgM in plants
Proc. Natl. Acad. Sci. USA 111 (2014) 6263 - 6268
doi: 10.1073/pnas.1320544111


96.

A. Schwaighofer, M. Pechlaner, C. Oostenbrink, C. Kotlowski; C. Araman, R. Mastrogiacomo, P. Pelosi, W. Knoll, M. Larisika; C. Nowak
Insights into structural features determining odorant affinities to honey bee odorant-binding protein 14
Biochem. Biophys. Res. Commun. 446 (2014) 1042–1046
doi: 10.1016/j.bbrc.2014.03.054


95.

Z. Lin, C. Oostenbrink, W.F. van Gunsteren
On the use of one-step perturbation to investigate the dependence of NOE derived atom-atom distance bound violations of peptides upon a variation of force-field parameters
Eur. Biophys. J. 43 (2014) 113 - 119
doi: 10.1007/s00249-014-0943-3


94.




J.A. Garate, T. Perez-Acle and C. Oostenbrink
On the thermodynamics of carbon nanotube single-file water loading: Free energy, Energy and Entropy calculations
Phys. Chem. Chem. Phys. 16 (2014) 5119 - 5128
doi: 10.1039/C3CP54554G


93.



B. Lai, C. Hasenhindl, C. Obinger and C. Oostenbrink
Molecular dynamics simulation of the crystallizable fragment of IgG1 – Insights for the design of Fcabs
Int. J. Mol. Sci. 15 (2014) 438-455
doi:10.3390/ijms15010438


92.



B. Lai, G. Nagy, J.A. Garate and C. Oostenbrink
Entropic and enthalpic contributions to stereospecific ligand binding from enhanced sampling methods
J. Chem. Inf. Model. 54 (2014) 151 – 158
doi: 10.1021/ci4006657


91.



G. Nagy and C. Oostenbrink
Dihedral-based segment identification and classification of biopolymers II: Polynucleotides
J. Chem. Inf. Model. 54 (2014) 278 – 288
doi: 10.1021/ci400542n


90.



G. Nagy and C. Oostenbrink
Dihedral-based segment identification and classification of biopolymers I: Proteins
J. Chem. Inf. Model. 54 (2014) 266 – 277
doi: 10.1021/ci400541d


89.




M.M. Reif and C. Oostenbrink
Net charge changes in the calculation of relative ligand-binding free energies via classical atomistic molecular dynamics simulation
J. Comput. Chem. 35 (2014) 227–243
doi: 10.1002/jcc.23490


88.



L. Peric-Hassler, E. Stjernschantz, C. Oostenbrink and D.P. Geerke
CYP 2D6 binding affinity predictions using multiple ligand and protein conformations
Int. J. Mol. Sci. 14 (2013) 24514-24530
doi: 10.3390/ijms141224514


87.





D. Artner, A. Oblak, S. Ittig, J.A. Garate, S. Horvat, C. Arrieumerlou, A. Hofinger, C. Oostenbrink, R. Jerala, P. Kosma and A. Zamyatina
Conformationally Constrained Lipid A Mimetics for Exploration of Structural Basis of TLR4/MD-2 Activation by Lipopolysaccharide
ACS Chem. Biol. 8 (2013) 2423−2432
doi: 10.1021/cb4003199


86.





C. Zou, M. Larisika, G. Nagy, J. Srajer, C. Oostenbrink, X. Chen, W. Knoll, B. Liedberg, C. Nowak
Two-dimensional heterospectral correlation analysis of the redox-induced conformational transition in Cytochrome c using surface-enhanced Raman and infrared absorption spectroscopies on a two-layer gold surface
J. Phys. Chem. B 117 (2013) 9606 - 9614
doi: 10.1021/jp404573q


85.

D. Petrov, C. Margreitter, M. Grandits, C. Oostenbrink, B. Zagrovic
A Systematic Framework for Molecular Dynamics Simulations of Protein Posttranslational Modifications
PLOS Comput. Biol. 9 (2013) e1003154
doi:10.1371/journal.pcbi.1003154


84.

A. Sündermann and C. Oostenbrink
Molecular dynamics simulations give insight into the conformational change, complex formation and electron transfer pathway for cytochrome P450 reductase
Protein Science 22 (2013) 1183 - 1195
doi: 10.1002/pro.2307


83.

M. M. H. Graf, U. Bren, D. Haltrich and C. Oostenbrink
Molecular dynamics simulations give insight into D-glucose dioxidation at C2 and C3 by Agaricus meleagris pyranose dehydrogenase
J. Comp-Aided Mol. Des. 27 (2013) 295 - 304
doi: 10.1007/s10822-013-9645-7


82.

M. Grandits, H. Michlmayr, C. Sygmund and C. Oostenbrink
Calculation of substrate binding affinities for a bacterial GH78 rhamnosidase through molecular dynamics simulations
Mol. Catal. B. 92 (2013) 34-43
doi: 10.1016/j.molcatb.2013.03.012


81.



J.A. Garate and C. Oostenbrink
Free energy differences between states with different conformational ensembles
J. Comput. Chem. 34 (2013) 1398 - 1408
doi: 10.1002/jcc.23276


80.

A. de Ruiter, S. Boresch and C. Oostenbrink
Comparison of thermodynamic integration and Bennett’s acceptance ratio for calculating relative protein – ligand binding free energies
J. Comput. Chem 34 (2013) 1024 - 1034
doi: 10.1002/jcc.23229


79.

M.M. Reif, M. Winger and C. Oostenbrink
Testing of the GROMOS force-field parameter set 54A8: Structural properties of electrolyte solutions, lipid bilayers and proteins
J. Chem. Theory Comput. 9 (2013) 1247 - 1264
DOI: 10.1021/ct300874c


78.

A. de Ruiter and C. Oostenbrink
Protein-ligand binding from distancefield distances and Hamiltonian replica exchange simulations
J. Chem. Theory Comp. 9 (2013) 883 - 892
doi: 10.1021/ct300967a


77.

J.A. Garate and C. Oostenbrink
Lipid A from lipopolysaccharide recognition: Structure, dynamics and cooperativity by molecular dynamics simulation
Proteins 81 (2013) 658 - 674
doi: 10.1002/prot.24223


76.

S. Hofbauer, M. Bellei, A. Sündermann, K.F. Pirker, A. Hagmüller, G. Mlynek, J. Kostan, H. Daims, P.G. Furtmüller, K. Djinović-Carugo, C. Oostenbrink, G. Battistuzzi and C.Obinger
Redox thermodynamics of high-spin and low-spin forms of chlorite dismutases of diverse subunit and oligomeric structure
Biochemistry 51 (2012) 9501 - 9512
doi: 10.1021/bi3013033


75.

G. Nagy and C. Oostenbrink
Rationalization of Sterospecific Binding of Propanolol to Cytochrome P450 2D6 by Free Energy Calculations
Eur. Biophys. J. 41 (2012) 1065 - 1076
doi: 10.1007/s00249-012-0865-x


74.

M.M. Reif, L. Mach and C. Oostenbrink
Molecular insight into propeptide-protein interactions in cathepsins L and O
Biochemistry 51 (2012) 8636−8653
doi: 10.1021/bi300802a


73.

B. Lai and C. Oostenbrink
Binding free energy, energy and entropy calculations using simple model systems
Theor. Chem. Acc.131 (2012) 1272
doi: 10.1007/s00214-012-1272-1


72.

S.B.A. de Beer, H. Venkataraman, D.P. Geerke, C. Oostenbrink and N.P.E. Vermeulen
Free energy calculations give insight into the stereoselective hydroxylation of α-ionones by engineered Cytochrome P450 BM3 mutants
J.Chem. Inf. Model. 52 (2012) 2139 - 2148
doi: 10.1021/ci300243n


71.

U. Bren and C. Oostenbrink
Cytochrome P450 3A4 Inhibition by Ketoconazole: Tackling the Problem of Ligand Cooperativity Using Molecular Dynamics Simulations and Free-Energy Calculations
J. Chem. Inf. Model. 52 (2012) 1573 - 1582
doi: 10.1021/ci300118x


70.

M.M. Reif, P. Hünenberger and C. Oostenbrink
New interaction parameters for charged amino acid side chains in the GROMOS force field
J. of Chem. Theory and Comp. 8 (2012) 3705 - 3723
doi: 10.1021/ct300156h



69.




R. Gößler-Schöfberger, G. Hesser, M.M. Reif, J. Friedmann, B. Duscher, J.L. Toca-Herrera, C. Oostenbrink, A. Jilek
A stereochemical switch in the aDrs model system, a candidate for a functional amyloid
Arch. Biochem. Biophys. 522 (2012) 100 - 106
doi: 10.1016/j.abb.2012.04.006


68.



D. Steiner, C. Oostenbrink and W.F. van Gunsteren
Calculation of the Relative Free Energy of Oxidation of Azurin at pH 5 and pH 9
J. Comput. Chem. 33 (2012) 1467 - 1477
doi: 10.1002/jcc.22972


67.



A. de Ruiter and C. Oostenbrink
Efficient and accurate free energy calculations on trypsin inhibitors
J. Chem. Theory Comp. 8 (2012) 3686 - 3695
doi: 10.1021/ct200750p


66.


C. Oostenbrink, A. de Ruiter, J. Hritz and N. Vermeulen
Malleability and Versatility of Cytochrome P450 Active Sites Studied by Molecular Simulations
Current Drug Metabolism, 13 (2012) 190 - 196


65.



C. Oostenbrink
„Free energy calculations from one-step perturbations“ in „Methods in Molecular Biology“, “Computational Drug Discovery and Design”, Vol. 819
Humana Press, New York, 487 - 499, (2012)


64.



A.K. Malde, Le Zuo, M. Breeze, M. Stroet, D. Poger, P.C. Nair. C. Oostenbrink, and A.E. Mark
An Automated Force Field Topology Builder (ATB) and Repository: Version 1.0
J. Chem. Theory Comp. 7 (2011 ) 4026 – 4037
doi: 10.1021/ct200196m


63.





S. Riniker, C.D. Christ, H.S. Hansen, P.H. Hünenberger, C. Oostenbrink, D. Steiner and W.F. van Gunsteren
Calculation of relative free energies for ligand-protein binding, solvation and conformational transitions using the GROMOS software
J. Phys. Chem. B 115 (2011) 13570 - 13577
doi: 10.1021/jp204303a


62.




A.P. Eichenberger, J.R. Allison, J. Dolenc, D.P. Geerke, B.A.C. Horta, K. Meier, C. Oostenbrink, N. Schmid, D. Steiner, D. Wang and W.F. van Gunsteren
GROMOS++ Software for the Analysis of Biomolecular Simulation Trajectories
J. Chem. Theory Comp. 7 (2011) 3379 - 3390
doi: 10.1021/ct2003622


61.





J.H.M. Lange, J. Venhorst, M.J.P. van Dongen, J. Frankena, F. Bassissi, N.M.W.J. de Bruin, C. den Besten, S.B.A. de Beer, C. Oostenbrink, N. Markova and C.G. Kruse
Biophysical and physicochemical methods differentiate highly ligand-efficient human D-amino acid oxidase inhibitors
Eur. J. Med. Chem. 46 (2011) 4808 - 4819
doi: 10.1016/j.ejmech.2011.04.023


60.




P. Vasanthanathan, J. Lastdrager, C. Oostenbrink, J.N.M. Commandeur, N.P.E. Vermeulen, F.S. Jorgensen, L. Olsen
Identification of CYP1A2 ligands by structure-based virtual screening
Med. Chem. Commun. 2 (2011) 853 - 859
doi: 10.1039/c1md00087j


59.



A. de Ruiter and C. Oostenbrink
Free energy calculations of protein-ligand interactions
Curr. Opin. Chem. Biol. 15 (2011) 547 - 552
doi: 10.1016/j.cbpa.2011.05.021


58.


A. de Ruiter, A. Mader, R. Kunert and C. Oostenbrink
Molecular simulations to rationalize humanized Ab2/3H6 activity
Aust. J. Chem. 64 (2011) 900 - 909


57.



S.B.A. de Beer, A. Glättli, J. Hutzler, N.P.E. Vermeulen and C. Oostenbrink
Molecular dynamics simulations and free energy calculations on the enzyme 4-hydroxyphenylpyruvate dioxygenase
J. Comput. Chem. 32 (2011) 2160 - 2169


56.


D. Steiner, C. Oostenbrink, F. Diederich, M. Zürcher, W.F. van Gunsteren
Calculation of binding free energies of inhibitors to plasmepsin II
J. Comput. Chem. 32 (2011) 1801 - 1812


55.



J. Hritz, T. Läppchen, C. Oostenbrink
Calculations of binding affinity between C8-substituted GTP analogs and the bacterial cell-division protein FtsZ
Eur. Biophys. J. 29 (2010) 1573 - 1580


54.



P. Vasanthanathan, L. Olsen, F.S. Jorgensen, N.P.E. Vermeulen, C. Oostenbrink
Computational prediction of binding affinity for CYP1A2-ligand complexes using empirical free energy calculations
Drug Metab. Disp. 38 (2010) 1347 - 1354


53.


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


52.



E. Stjernschantz, J. Reinen, W. Meinl, B.J. George, H. Glatt, N.P.E. Vermeulen, C. Oostenbrink
Comparison of murine and human estrogen sulfotransferase inhibition in vitro and in silico - implications for differences in activity, subunit dimerization and substrate inhibition
Mol. Cell. Endocrinol. 317 (2010) 127 - 140


51.


T. Venäläinen, F. Molnar, C. Oostenbrink, C. Carlberg and M. Peräkylä
Molecular mechanism of allosteric communication in the human PPARalpha-RXRalpha heterodimer
Proteins 78 (2010) 873 - 887


50.


R. Santos, J. Hritz and C. Oostenbrink
The role of water in molecular docking simulations of Cytochrome P450 2D6
J. Chem. Inf. Model 50 (2010) 146 - 154


49.


S.B.A. de Beer, N.P.E. Vermeulen and C. Oostenbrink
The role of water molecules in computational drug design
Curr. Top. Med. Chem. 10 (2010) 55 - 66


48.


G. Zoldak, T. Aumüller, C. Lücke, J. Hritz, C. Oostenbrink, G. Fischer, F.X. Schmid
A library of fluorescent peptides for exploring the substrate specificities of prolyl isomerases
Biochemistry 48 (2009) 10423 - 10436


47.


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


46.



J. Hritz and C. Oostenbrink
Efficient free energy calculations for compounds with multiple stable conformations separated by high energy barriers
J. Phys. Chem. B. 113 (2009) 12711 - 12720


45.


P. Vasanthanathan, O. Taboureau, C. Oostenbrink, N.P.E. Vermeulen, L. Olsen and F.S. Jorgensen
Classification of Cytochrome P450 1A2 Inhibitors and Non-Inhibitors by Machine Learning Techniques
Drug Metab. Disp. 37 (2009) 658 - 664


44.



P. Vasanthanathan, J. Hritz, O. Taboureau, L. Olsen and F.S. Jorgensen, N.P.E. Vermeulen and C. Oostenbrink
Virtual screening and prediction of site of metabolism for cytochrome P450 1A2 ligands
J. Chem. Inf. Model. 49 (2009) 43 - 52


43.



C. Oostenbrink
Efficient free energy calculations on small molecule host-guest systems - a combined Linear Interaction Energy / One-Step perturbation approach
J. Comput. Chem. 30 (2009) 212 - 221


42.



J. Hritz, A. de Ruiter and C. Oostenbrink
Impact of plasticity and flexibility on docking results for Cytochrome P450 2D6: a combined approach of molecular dynamics and ligand docking
J. Med. Chem. 51 (2008) 7469 - 7477


41.


E. Stjernschantz, N.P.E. Vermeulen and C. Oostenbrink
Computational prediction of drug binding and rationalisation of selectivity towards Cytochromes P450
Expert Opin. Drug Metab. Toxicol. 4 (2008) 513 - 527


40.


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


39.



E. Stjernschantz, B.M.A. van Vugt-Lussenburg, A. Bonifacio, S.B.A. de Beer, G. van der Zwan, C. Gooijer, J.N.M. Commandeur, N.P.E. Vermeulen and C. Oostenbrink
Structural rationalization of novel drug metabolizing mutants of cytochrome P450 BM3
Proteins 71 (2008) 336 - 352


38.


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


37.



W.F. van Gunsteren, D.P. Geerke, D. Trzesniak, C. Oostenbrink and N.F.A. van der Vegt
Analysis of the driving forces for biomolecular solvation and association
Proc. Italian School of Physics "Enrico Fermi", Course CLXV, R.A. Broglia, L. Serrano and G. Tiana (Eds.), IOS Press, Amsterdam - SIF, Bologna (2007) 177 - 191


36.




C. de Graaf, C. Oostenbrink, P.H.J. Keizers, B.M.A. van Vugt-Lussenburg, J.N.M. Commandeur, N.P.E. Vermeulen
Free energies of binding of R- and S-propranolol to wildtype and F483A mutant Cytochrome P450 2D6 from molecular dynamics simulations
Eur. Biophys. J. 36 (2007) 589 - 599


35.



C. Oostenbrink, M.M.H. van Lipzig and W.F. van Gunsteren
Applications of molecular dynamics simulations in drug design
In: "Comprehensive Medicinal Chemistry II" Vol. 4, Computer-Assisted Drug Design, J.B. Taylor and D.J. Triggle Eds., Elsevier, Amsterdam, 2007, pp 651-668


34.




B.M.A. van Vugt-Lussenburg, E. Stjernschantz, J. Lastdrager, C. Oostenbrink, N.P.E. Vermeulen and J.N.M. Commandeur
Identification of novel critical residues in drug metabolising mutants of Cytochrome P450 BM3 using random mutagenesis
J. Med. Chem. 50 (2007) 455 - 461


33.


B. Keller, M. Christen, C. Oostenbrink, W.F. van Gunsteren
On using oscillating time-dependent restraints in MD simulation
J. Biomol. NMR 37 (2007) 1 - 14


32.



C. de Graaf, C. Oostenbrink, P. Keizers, B. van Vugt-Lussenburg, R. van Waterschoot, R. Tschirret-Guth, J. Commandeur, N.P.E. Vermeulen
Molecular modeling-guided site-directed mutagenesis of cytochrome P450 2D6
Curr. Drug. Metab. 8 (2007) 59 - 77


31.



E. Stjernschantz, J. Marelius, C. Medina, M. Jacobsson, N.P.E. Vermeulen and Chris Oostenbrink
Are automated molecular dynamics simulations and binding free energy calculations realistic tools in lead optimization? - An evaluation of the linear interaction energy (LIE) method
J. Chem. Inf. Model. 46 (2006) 1972 - 1983


30.


J. Dolenc, R. Baron, C. Oostenbrink, J. Koller and W.F. van Gunsteren
Configurational entropy change of netropsin and distamycin upon DNA minor-groove binding
Biophys. J. 91 (2006) 1460 - 1470


29.





W.F. van Gunsteren, D. Bakowies, R. Baron, I. Chandrasekhar, M. Christen, X. Daura, P.Gee, D.P. Geerke, A. Glättli, P.H. Hünenberger, M.A. Kastenholz, C. Oostenbrink, M. Schenk, D. Trzesniak, N.F.A. van der Vegt and H.B. Yu
Biomolecular modeling: goals, problems, perspectives
Angew. Chem 118 (2006) 4168-4198
Angew. Chem. Int. Ed. 45 (2006) 4064-4092


28.



C. de Graaf, C. Oostenbrink, P.H.J. Keizers, T. van der Wijst, A. Jongejan, N.P.E. Vermeulen
Catalytic site prediction and virtual screening of cytochrome P450 2D6 substrates by consideration of water and rescoring in automated docking
J. Med. Chem. 49 (2006) 2417 - 2430


27.



Y. Zhou, C. Oostenbrink, A. Jongejan, W.F. van Gunsteren, W.R. Hagen, S.W. de Leeuw, J.A. Jongejan
Computational study of ground state chiral induction in small peptides: Comparison of the relative stability of selected amino acid dimers and oligomers in homochiral and heterochiral combinations
J. Comput. Chem. 27 (2006) 857-867


26.


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


25.




A. Stortelder, P.H.J. Keizers, C. Oostenbrink, C. de Graaf, P. de Kruijf, N.P.E. Vermeulen, C. Gooijer, J.N.M. Commandeur, G. van der Zwan
Binding of 7-methoxy-4-(aminomethyl)-coumarin to wild-type and W128F mutant cytochrome P450 2D6 studied by time-resolved fluorescence spectroscopy
Biochem. J., 393 (2006) 635 - 643


24.



M. Christen, D. Bakowies, R. Baron, R. Bürgi, D. Geerke, T. Heinz, P. Hünenberger, M. Kastenholz, V. Kräutler, C. Oostenbrink, C. Peter, D. Trzesniak and W.F. van Gunsteren
The GROMOS software for biomolecular simulation: GROMOS05
J. Comput. Chem., 26 (2005) 1719 - 1751


23.


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


22.




P.H.J. Keizers, C. de Graaf, F.J.J. de Kanter, C. Oostenbrink, K.A. Feenstra, J.N.M. Commandeur and N.P.E. Vermeulen
Metabolic regio- and stereoselectivity of cytochrome P450 2D6 towarSubmitted to J.Chem. Inf. Model. (2012)ds 3,4-methylenedioxy-N-alkylamphetamines: in silico predictions and experimental validation
J. Med. Chem., 48 (2005) 6117 - 6127


21.


C. Oostenbrink and W.F. van Gunsteren
Efficient calculation of stacking and pairing free energies in DNA from molecular dynamics simulations
Chem. Eur. J., 11 (2005) 4340 - 4348


20.



Y. Zhou, C. Oostenbrink, W.F. van Gunsteren, W.R. Hagen, S.R. de Leeuw, J. Jongejan
Relative stability of homochiral and heterochiral dialanine peptides. Effects of perturbation pathways and force-field parameters on free energy calculations
Mol. Phys., 104 (2005) 1961 - 1969


19.


C. Oostenbrink, T.A. Soares, N.F.A. van der Vegt and W.F. van Gunsteren
Validation of the 53A6 GROMOS force field
Eur. Biophys. J., 34 (2005) 273 - 284


18.


C. Oostenbrink and W.F. van Gunsteren
Free energies of ligand binding for structurally diverse compounds
Proc. Natl. Acad. Sci. USA, 102 (2005) 6750 - 6754


17.



M. van den Bosch, M. Swart, J. Snijders, H.J.C. Berendsen, A.E. Mark, C. Oostenbrink, W.F. van Gunsteren and G.W. Canters
Calculation of the redox potential of the protein azurin and some mutants
ChemBioChem, 6 (2005) 738 - 746


16.



T.A. Soares, P.H. Hünenberger, M.A. Kastenholz, V. Kräutler, T. Lenz, R.D. Lins, C. Oostenbrink and W.F. van Gunsteren
An improved nucleic-acid parameter set for the GROMOS force field
J. Comput. Chem., 26 (2005) 725 - 737


15.


J. Dolenc, C. Oostenbrink, J. Koller, W.F. van Gunsteren
Relative free energies of binding of Netropsin and Distamycin A to DNA
Nucl. Acid Res., 33 (2005) 725 - 733


14.



T.A. Soares, X. Daura, C. Oostenbrink, L.J. Smith, W.F. van Gunsteren
Validation of the GROMOS Force-field Parameter Set 45A3 against Nuclear Magnetic Resonance Data of Hen Egg Lysozyme
J. Biomol. NMR, 30 (2004) 407 - 422


13.


C. Oostenbrink and W.F. van Gunsteren
Methane clustering in explicit water: Effect of urea on hydrophobic interactions
Phys. Chem. Chem. Phys. 7 (2005) 53 - 58


12.



C. Oostenbrink, A. Villa, A.E. Mark and W.F. van Gunsteren
A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6
J. Comp. Chem. 25 (2004) 1656 - 1676


11.


I. Chandrasekhar, C. Oostenbrink and W.F. van Gunsteren
Simulating the Physiological Phase of Hydrated Dipalmitoylphosphatidylcholine Bilayers: The Ester Moiety
Soft Materials 2 (2004) 27 - 45


10.


A. Glättli, C. Oostenbrink, X. Daura, D.P. Geerke, H. Yu, W.F. van Gunsteren
On the transferability of the SPC/L water model to biomolecular simulation
Brazilian J. of Phys. 34 (2004) 116-125


9.


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


8.



D.P. Geerke, C. Oostenbrink, N.F.A. van der Vegt and W.F. van Gunsteren
An Effective Force Field for Molecular Dynamics Simulations of Dimethyl Sulfoxide and Dimethyl Sulfoxide-Water Mixtures
J. Phys. Chem. B 108 (2004) 1436 - 1445


7.


C. Oostenbrink and W.F. van Gunsteren
Free energies of binding of polychlorinated biphenyls to the estrogen receptor from a single simulation
Proteins 54 (2004) 234-246


6.



C. Oostenbrink and W.F. van Gunsteren
Single-step perturbations to calculate free energy differences from unphysical reference states: limits on size, flexibility and character
J. Comput. Chem. 24 (2003) 1730-1739


5.




I. Chandrasekhar, M. Kastenholz, R.D. lins, C. Oostenbrink, L.D. Schuler, D.P. Tieleman and W.F. van Gunsteren
A consistent potential energy parameter set for lipids: Dipalmitoylphosphatidylcholine as a benchmark of the GROMOS96 45A3 force field
Europ. Biophys. J. 32 (2003) 67-77


4.


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


3.


V.P. Osinga, B.C. Oostenbrink, E. van Lenthe, C. Fonseca Guerra, E.J. Baerends
A least squares multicenter approach to continuum wave functions
Chem. Phys. 284 (2002) 565 - 574


2.



W.F. van Gunsteren, D. Bakowies, R. Bürgi, I. Chandrasekhar, M. Christen, X. Daura, P. Gee, A. Glättli, T. Hansson, C. Oostenbrink, C. Peter, J. Pitera, L. Schuler, T. Soares and H. Yu
Molecular Dynamics Simulation of Biomolecular Systems
CHIMIA 55 (2001) 856-860


1.



B.C. Oostenbrink, J.W. Pitera, M.M.H. van Lipzig, J.H.N. Meerman and W.F. van Gunsteren
Simulations of the Estrogen Receptor Ligand Binding Domain: the affinity of natural ligands and xenoestrogens
J. Med. Chem. 43 (2000) 4594-4605


Publikationen in Druck

veröffentlicht

a.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
Submitted to ChemBioChem (2017)
b.D. Vojta, 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
Submitted to Chemistry and Physics of Lipids (2017)
c.G. Wagner-Lichtenegger, H. Hofbauer, W. Hohlweg, M. Setz, N. Gubensäk, S. Lichtenegger, F. Falsone, H. Wolinski, S. Kosol, C. Oostenbrink, S. Kohlwein, K. Zangger A cation-π interaction in a transmembrane helix of vacuolar ATPase keeps the proton transporting arginine in a hydrophobic environment
Submitted to Angew. Chemie (2017)

d.J.W. Perthold and C. Oostenbrink
Simulation of Reversible Protein-Protein Binding and Calculation of Binding Free Energies using Perturbed Distance Restraints
Submitted to J. Chem. Theory Comput. (2017)