Chris Oostenbrink - Publications

Affiliations: 
Eidgenössische Technische Hochschule Zürich, Zürich, ZH, Switzerland 
 Institute for Molecular Modeling and Simulation (MMS) Boku University Vienna, Austria 
Website:
https://boku.ac.at/en/map/mms

204 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Kröß C, Engele P, Sprenger B, Fischer A, Lingg N, Baier M, Öhlknecht C, Lier B, Oostenbrink C, Cserjan-Puschmann M, Striedner G, Jungbauer A, Schneider R. PROFICS: A bacterial selection system for directed evolution of proteases. The Journal of Biological Chemistry. 101095. PMID 34418435 DOI: 10.1016/j.jbc.2021.101095  1
2021 Hoffmann D, Mereiter S, Jin Oh Y, Monteil V, Elder E, Zhu R, Canena D, Hain L, Laurent E, Grünwald-Gruber C, Klausberger M, Jonsson G, Kellner MJ, Novatchkova M, Ticevic M, ... ... Oostenbrink C, et al. Identification of lectin receptors for conserved SARS-CoV-2 glycosylation sites. The Embo Journal. e108375. PMID 34375000 DOI: 10.15252/embj.2021108375  1
2021 Sebastiani F, Michlits H, Lier B, Becucci M, Furtmüller PG, Oostenbrink C, Obinger C, Hofbauer S, Smulevich G. Reaction intermediate rotation during the decarboxylation of coproheme to heme b in C.diphtheriae. Biophysical Journal. PMID 34339636 DOI: 10.1016/j.bpj.2021.06.042  1
2021 Galicia-Andrés E, Tunega D, Gerzabek MH, Oostenbrink C. On glyphosate-kaolinite surface interactions. A molecular dynamic study. European Journal of Soil Science. 72: 1231-1242. PMID 34220276 DOI: 10.1111/ejss.12971  1
2021 Pechlaner M, Oostenbrink C, van Gunsteren WF. On the use of multiple-time-step algorithms to save computing effort in molecular dynamics simulations of proteins. Journal of Computational Chemistry. PMID 33951201 DOI: 10.1002/jcc.26541  1
2021 Gotsmy M, Escalona Y, Oostenbrink C, Petrov D. Exploring the structure and dynamics of proteins in soil organic matter. Proteins. PMID 33675059 DOI: 10.1002/prot.26070  1
2021 Öhlknecht C, Katz S, Kröß C, Sprenger B, Engele P, Schneider R, Oostenbrink C. Efficient Saturation Mutagenesis of a Member of the Caspase Protease Family. Journal of Chemical Information and Modeling. PMID 33570387 DOI: 10.1021/acs.jcim.0c01216  0.01
2021 Felice AKG, Schuster C, Kadek A, Filandr F, Laurent CVFP, Scheiblbrandner S, Schwaiger L, Schachinger F, Kracher D, Sygmund C, Man P, Halada P, Oostenbrink C, Ludwig R. Chimeric Cellobiose Dehydrogenases Reveal the Function of Cytochrome Domain Mobility for the Electron Transfer to Lytic Polysaccharide Monooxygenase. Acs Catalysis. 11: 517-532. PMID 33489432 DOI: 10.1021/acscatal.0c05294  1
2020 van Gunsteren WF, Daura X, Fuchs PFJ, Hansen N, Horta BAC, Hünenberger PH, Mark AE, Pechlaner M, Riniker S, Oostenbrink C. On the Effect of the Various Assumptions and Approximations used in Molecular Simulations on the Properties of Bio-Molecular Systems: Overview and Perspective on Issues. Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry. PMID 33377305 DOI: 10.1002/cphc.202000968  1
2020 Roither B, Oostenbrink C, Pfeiler G, Koelbl H, Schreiner W. Pembrolizumab Induces an Unexpected Conformational Change in the CC'-loop of PD-1. Cancers. 13. PMID 33375020 DOI: 10.3390/cancers13010005  1
2020 de Ruiter A, Petrov D, Oostenbrink C. Optimization of Alchemical Pathways Using Extended Thermodynamic Integration. Journal of Chemical Theory and Computation. PMID 33351609 DOI: 10.1021/acs.jctc.0c01170  1
2020 Roither B, Oostenbrink C, Schreiner W. 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: 557. PMID 33308148 DOI: 10.1186/s12859-020-03904-9  1
2020 Escalona Y, Petrov D, Oostenbrink C. Vienna soil organic matter modeler 2 (VSOMM2). Journal of Molecular Graphics & Modelling. 103: 107817. PMID 33291027 DOI: 10.1016/j.jmgm.2020.107817  1
2020 Cserjan-Puschmann M, Lingg N, Engele P, Kröß C, Loibl J, Fischer A, Bacher F, Frank AC, Öhlknecht C, Brocard C, Oostenbrink C, Berkemeyer M, Schneider R, Striedner G, Jungbauer A. Production of Circularly Permuted Caspase-2 for Affinity Fusion-Tag Removal: Cloning, Expression in , Purification, and Characterization. Biomolecules. 10. PMID 33255244 DOI: 10.3390/biom10121592  1
2020 Lingg N, Öhlknecht C, Fischer A, Mozgovicz M, Scharl T, Oostenbrink C, Jungbauer A. Proteomics analysis of host cell proteins after immobilized metal affinity chromatography: Influence of ligand and metal ions. Journal of Chromatography. A. 1633: 461649. PMID 33166743 DOI: 10.1016/j.chroma.2020.461649  1
2020 Öhlknecht C, Perthold JW, Lier B, Oostenbrink C. Charge-Changing Perturbations and Path Sampling via Classical Molecular Dynamic Simulations of Simple Guest-Host Systems. Journal of Chemical Theory and Computation. PMID 33136389 DOI: 10.1021/acs.jctc.0c00719  1
2020 Petrov D, Tunega D, Gerzabek MH, Oostenbrink C. Molecular modelling of sorption processes of a range of diverse small organic molecules in Leonardite humic acid. European Journal of Soil Science. 71: 831-844. PMID 33041627 DOI: 10.1111/Ejss.12868  1
2020 Diem M, Oostenbrink C. The effect of different cutoff schemes in molecular simulations of proteins. Journal of Computational Chemistry. PMID 33026106 DOI: 10.1002/jcc.26426  1
2020 Diem M, Oostenbrink C. The effect of using a twin-range cut-off scheme for non-bonded interactions: Implications for force-field parameterization? Journal of Chemical Theory and Computation. PMID 32813524 DOI: 10.1021/Acs.Jctc.0C00509  1
2020 Yang S, Liu JDH, Diem M, Wesseling S, Vervoort J, Oostenbrink C, Rietjens IMCM. Molecular dynamics and in vitro quantification of safrole DNA adducts reveal DNA adduct persistence due to limited DNA distortion resulting in inefficient repair. Chemical Research in Toxicology. PMID 32786539 DOI: 10.1021/Acs.Chemrestox.0C00097  1
2020 Perthold JW, Petrov D, Oostenbrink C. Toward Automated Free Energy Calculation with Accelerated Enveloping Distribution Sampling (A-EDS). Journal of Chemical Information and Modeling. PMID 32492343 DOI: 10.1021/Acs.Jcim.0C00456  1
2020 Michlits H, Lier B, Pfanzagl V, Djinović-Carugo K, Furtmüller PG, Oostenbrink C, Obinger C, Hofbauer S. Actinobacterial Coproheme Decarboxylases Use Histidine as a Distal Base to Promote Compound I Formation. Acs Catalysis. 10: 5405-5418. PMID 32440366 DOI: 10.1021/Acscatal.0C00411  1
2020 Öhlknecht C, Petrov D, Engele P, Kröß C, Sprenger B, Fischer A, Lingg N, Schneider R, Oostenbrink C. Enhancing the promiscuity of a member of the Caspase protease family by rational design. Proteins. PMID 32432825 DOI: 10.1002/Prot.25950  1
2020 Breslmayr E, Laurent CVFP, Scheiblbrandner S, Jerkovic A, Heyes DJ, Oostenbrink C, Ludwig R, Hedison TM, Scrutton NS, Kracher D. Protein Conformational Change Is Essential for Reductive Activation of Lytic Polysaccharide Monooxygenase by Cellobiose Dehydrogenase. Acs Catalysis. 10: 4842-4853. PMID 32382450 DOI: 10.1021/Acscatal.0C00754  1
2020 Yang S, Diem M, Liu JDH, Wesseling S, Vervoort J, Oostenbrink C, Rietjens IMCM. Cellular levels and molecular dynamics simulations of estragole DNA adducts point at inefficient repair resulting from limited distortion of the double-stranded DNA helix. Archives of Toxicology. PMID 32185416 DOI: 10.1007/S00204-020-02695-5  1
2020 Gladović M, Oostenbrink C, Bren U. Could Microwave Irradiation Cause Misfolding of Peptides? Journal of Chemical Theory and Computation. PMID 32163704 DOI: 10.1021/Acs.Jctc.9B01104  1
2020 de Ruiter A, Oostenbrink C. Advances in the calculation of binding free energies. Current Opinion in Structural Biology. 61: 207-212. PMID 32088376 DOI: 10.1016/J.Sbi.2020.01.016  1
2020 Öhlknecht C, Lier B, Petrov D, Fuchs J, Oostenbrink C. Correcting electrostatic artifacts due to net-charge changes in the calculation of ligand binding free energies. Journal of Computational Chemistry. PMID 31930547 DOI: 10.1002/Jcc.26143  1
2020 Galicia‐Andrés E, Tunega D, Gerzabek MH, Oostenbrink C. On glyphosate‐kaolinite surface interactions. A molecular dynamic study European Journal of Soil Science. DOI: 10.1111/Ejss.12971  1
2019 Diem M, Oostenbrink C. Hamiltonian Reweighing to refine Protein Backbone Dihedral-Angle Parameters in the GROMOS Force Field. Journal of Chemical Information and Modeling. PMID 31873012 DOI: 10.1021/Acs.Jcim.9B01034  1
2019 Turupcu A, Blaukopf M, Kosma P, Oostenbrink C. Molecular Conformations of Di-, Tri-, and Tetra--(2→8)-Linked Sialic Acid from NMR Spectroscopy and MD Simulations. International Journal of Molecular Sciences. 21. PMID 31861593 DOI: 10.3390/Ijms21010030  1
2019 Laurent CVFP, Sun P, Scheiblbrandner S, Csarman F, Cannazza P, Frommhagen M, van Berkel WJH, Oostenbrink C, Kabel MA, Ludwig R. Influence of Lytic Polysaccharide Monooxygenase Active Site Segments on Activity and Affinity. International Journal of Molecular Sciences. 20. PMID 31835532 DOI: 10.3390/Ijms20246219  1
2019 Breslmayr E, Daly S, Požgajčić A, Chang H, Rezić T, Oostenbrink C, Ludwig R. Improved spectrophotometric assay for lytic polysaccharide monooxygenase. Biotechnology For Biofuels. 12: 283. PMID 31827611 DOI: 10.1186/S13068-019-1624-3  1
2019 Perthold JW, Oostenbrink C. GroScore: Accurate Scoring of Protein-Protein Binding Poses using Explicit-Solvent Free-Energy Calculations. Journal of Chemical Information and Modeling. PMID 31790223 DOI: 10.1021/Acs.Jcim.9B00687  1
2019 Galicia-Andrés E, Petrov D, Gerzabek MH, Oostenbrink C, Tunega D. Polarization effects in simulations of kaolinite-water interfaces. Langmuir : the Acs Journal of Surfaces and Colloids. PMID 31663747 DOI: 10.1021/Acs.Langmuir.9B02945  1
2019 Maurer M, Oostenbrink C. Water in protein hydration and ligand recognition. Journal of Molecular Recognition : Jmr. e2810. PMID 31456282 DOI: 10.1002/Jmr.2810  1
2019 Milazzo L, Gabler T, Pühringer D, Jandova Z, Maresch D, Michlits H, Pfanzagl V, Djinović-Carugo K, Oostenbrink C, Furtmüller PG, Obinger C, Smulevich G, Hofbauer S. Redox Cofactor Rotates during Its Stepwise Decarboxylation: Molecular Mechanism of Conversion of Coproheme to Heme . Acs Catalysis. 9: 6766-6782. PMID 31423350 DOI: 10.2210/Pdb6Fxj/Pdb  1
2019 Turupcu A, Poliak P, Margreitter C, Oostenbrink C, Staudacher E. UDP-N-acetyl-α-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase from the snail Biomphalaria glabrata - structural reflections. Glycoconjugate Journal. PMID 31396754 DOI: 10.1007/S10719-019-09886-Y  1
2019 Göritzer K, Turupcu A, Maresch D, Novak J, Altmann F, Oostenbrink C, Obinger C, Strasser R. Distinct Fc alpha receptor N-glycans modulate the binding affinity to immunoglobulin A (IgA) antibodies. The Journal of Biological Chemistry. PMID 31362986 DOI: 10.1074/Jbc.Ra119.009954  1
2019 Schwaigerlehner L, Mayrhofer P, Diem M, Steinfellner W, Fenech E, Oostenbrink C, Kunert R. Germinality does not necessarily define mAb expression and thermal stability. Applied Microbiology and Biotechnology. PMID 31350616 DOI: 10.1007/S00253-019-09998-3  1
2019 Pfanzagl V, Bellei M, Hofbauer S, Laurent CVFP, Furtmüller PG, Oostenbrink C, Battistuzzi G, Obinger C. Redox thermodynamics of B-class dye-decolorizing peroxidases. Journal of Inorganic Biochemistry. 199: 110761. PMID 31325671 DOI: 10.1016/J.Jinorgbio.2019.110761  1
2019 Jandova Z, Jespers W, Sotelo E, Gutiérrez-de-Terán H, Oostenbrink C. Free-Energy Calculations for Bioisosteric Modifications of A Adenosine Receptor Antagonists. International Journal of Molecular Sciences. 20. PMID 31315296 DOI: 10.3390/Ijms20143499  1
2019 Turupcu A, Bowen AM, Di Paolo A, Matagne A, Oostenbrink C, Redfield C, Smith LJ. An NMR and MD Study of Complexes of Bacteriophage Lambda Lysozyme with Tetra- and Hexa-N-acetylchitohexaose. Proteins. PMID 31294851 DOI: 10.1002/Prot.25770  1
2019 Jandova Z, Gill SC, Lim NM, Mobley DL, Oostenbrink C. Binding modes and metabolism of caffeine. Chemical Research in Toxicology. PMID 31132250 DOI: 10.1021/Acs.Chemrestox.9B00030  1
2019 Turupcu A, Diem M, Smith LJ, Oostenbrink C. Structural Aspects of the O-glycosylation Linkage in Glycopeptides via MD Simulations and Comparison with NMR Experiments. Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry. 20: 1527-1537. PMID 30920077 DOI: 10.1002/Cphc.201900079  1
2019 Vila-Viçosa D, Reis PBPS, Baptista AM, Oostenbrink C, Machuqueiro M. A pH Replica Exchange Scheme in the Stochastic Titration Constant-pH MD Method. Journal of Chemical Theory and Computation. 15: 3108-3116. PMID 30908045 DOI: 10.1021/Acs.Jctc.9B00030  1
2019 Laurent CVFP, Breslmayr E, Tunega D, Ludwig R, Oostenbrink C. Interaction between Cellobiose Dehydrogenase and Lytic Polysaccharide Monooxygenase. Biochemistry. 58: 1226-1235. PMID 30715860 DOI: 10.1021/Acs.Biochem.8B01178  1
2019 Schwaigerlehner L, Pechlaner M, Mayrhofer P, Oostenbrink C, Kunert R. Lessons learned from merging wet lab experiments with molecular simulation to improve mAb humanization. Protein Engineering, Design & Selection : Peds. 31: 257-265. PMID 29757445 DOI: 10.1093/Protein/Gzy009  0.04
2019 Ma S, Laurent CVFP, Meneghello M, Tuoriniemi J, Oostenbrink C, Gorton L, Bartlett PN, Ludwig R. Direct Electron-Transfer Anisotropy of a Site-Specifically Immobilized Cellobiose Dehydrogenase Acs Catalysis. 9: 7607-7615. DOI: 10.1021/Acscatal.9B02014  0.01
2019 Turupcu A, Oostenbrink C. In Search of a Structural Pattern in Crazy Sugarsidentification of Conformation Clusters of the Oligosaccharides Within Glycoproteins with LEUS Biophysical Journal. 116: 570a. DOI: 10.1016/J.Bpj.2018.11.3064  0.04
2018 Silva TFD, Vila-Viçosa D, Reis PBPS, Victor BL, Diem M, Oostenbrink C, Machuqueiro M. The impact of using single atomistic long range cutoff schemes with the GROMOS 54A7 force field. Journal of Chemical Theory and Computation. PMID 30354115 DOI: 10.1021/Acs.Jctc.8B00758  1
2018 Maurer M, Hansen N, Oostenbrink C. Comparison of free-energy methods using a tripeptide-water model system. Journal of Computational Chemistry. 39: 2226-2242. PMID 30280398 DOI: 10.1002/Jcc.25537  1
2018 Hohlweg W, Wagner GE, Hofbauer HF, Sarkleti F, Setz M, Gubensäk N, Lichtenegger S, Falsone SF, Wolinski H, Kosol S, Oostenbrink C, Kohlwein SD, Zangger K. A cation-π interaction in a transmembrane helix of vacuolar ATPase retains the proton transporting arginine in a hydrophobic environment. The Journal of Biological Chemistry. PMID 30209131 DOI: 10.1074/Jbc.Ra118.005276  1
2018 Turupcu A, Almohamed W, Oostenbrink C, Seifert GJ. A speculation on the tandem fasciclin 1 repeat of FLA4 proteins in angiosperms. Plant Signaling & Behavior. 13: e1507403. PMID 30148420 DOI: 10.1080/15592324.2018.1507403  1
2018 Margreitter C, Oostenbrink C. Correction to Optimization of Protein Backbone Dihedral Angles by Means of Hamiltonian Reweighting. Journal of Chemical Information and Modeling. 58: 1716-1720. PMID 30062876 DOI: 10.1021/Acs.Jcim.8B00470  1
2018 Porodko A, Cirnski A, Petrov D, Raab T, Paireder M, Mayer B, Maresch D, Nika L, Biniossek ML, Gallois P, Schilling O, Oostenbrink C, Novinec M, Mach L. The two cathepsin B-like proteases of Arabidopsis thaliana are closely related enzymes with discrete endopeptidase and carboxydipeptidase activities. Biological Chemistry. PMID 29924726 DOI: 10.1515/Hsz-2018-0186  1
2018 Perthold JW, Oostenbrink C. Accelerated Enveloping Distribution Sampling: Enabling Sampling of Multiple End States while Preserving Local Energy Minima. The Journal of Physical Chemistry. B. 122: 5030-5037. PMID 29669415 DOI: 10.1021/Acs.Jpcb.8B02725  1
2018 Breslmayr E, Hanžek M, Hanrahan A, Leitner C, Kittl R, Šantek B, Oostenbrink C, Ludwig R. A fast and sensitive activity assay for lytic polysaccharide monooxygenase. Biotechnology For Biofuels. 11: 79. PMID 29588664 DOI: 10.1186/S13068-018-1063-6  1
2018 Jandova Z, Fast D, Setz M, Pechlaner M, Oostenbrink C. Saturation Mutagenesis by Efficient Free-Energy Calculation. Journal of Chemical Theory and Computation. 14: 894-904. PMID 29262673 DOI: 10.1021/Acs.Jctc.7B01099  1
2018 Jandova Z, Trosanova Z, Weisova V, Oostenbrink C, Hritz J. Free energy calculations on the stability of the 14-3-3ζ protein. Biochimica Et Biophysica Acta. Proteins and Proteomics. 1866: 442-450. PMID 29203375 DOI: 10.1016/J.Bbapap.2017.11.012  1
2018 Bakarić D, Petrov D, Mouvenchery YK, Heiβler S, Oostenbrink C, Schaumann GE. Ion-induced modification of the sucrose network and its impact on melting of freeze-dried liposomes. DSC and molecular dynamics study. Chemistry and Physics of Lipids. 210: 38-46. PMID 29179944 DOI: 10.1016/J.Chemphyslip.2017.11.015  1
2017 Németh E, Asaka M, Kato K, Fabian Z, Oostenbrink C, Christensen H, Nagata K, Gyurcsik B. Chemical approach to biological safety - Molecular level control of an integrated zinc finger nuclease. Chembiochem : a European Journal of Chemical Biology. PMID 29077265 DOI: 10.1002/Cbic.201700420  1
2017 Perthold JW, Oostenbrink C. Simulation of Reversible Protein-Protein Binding and Calculation of Binding Free Energies Using Perturbed Distance Restraints. Journal of Chemical Theory and Computation. 13: 5697-5708. PMID 28898077 DOI: 10.1021/Acs.Jctc.7B00706  1
2017 Margreitter C, Oostenbrink C. MDplot: Visualise Molecular Dynamics. The R Journal. 9: 164-186. PMID 28845302 DOI: 10.32614/Rj-2017-007  1
2017 Turupcu A, Oostenbrink C. Modeling of Oligosaccharides within Glycoproteins from Free-Energy Landscapes. Journal of Chemical Information and Modeling. 57: 2222-2236. PMID 28816453 DOI: 10.1021/Acs.Jcim.7B00351  1
2017 Sergelen K, Fossati S, Turupcu A, Oostenbrink C, Liedberg B, Knoll W, Dostálek J. Plasmon Field-Enhanced Fluorescence Energy Transfer for Hairpin Aptamer Assay Readout. Acs Sensors. 2: 916-923. PMID 28750521 DOI: 10.1021/Acssensors.7B00131  1
2017 Nagy G, Oostenbrink C, Hritz J. Exploring the binding pathways of the 14-3-3ζ protein: Structural and free-energy profiles revealed by Hamiltonian replica exchange molecular dynamics with distancefield distance restraints. Plos One. 12: e0180633. PMID 28727767 DOI: 10.1371/Journal.Pone.0180633  1
2017 van Gunsteren WF, Daura X, Hansen N, Mark A, Oostenbrink C, Riniker S, Smith L. Validation of Molecular Simulation: An Overview of Issues. Angewandte Chemie (International Ed. in English). PMID 28682472 DOI: 10.1002/Anie.201702945  1
2017 Petrov D, Tunega D, Gerzabek MH, Oostenbrink C. Molecular Dynamics Simulations of the Standard Leonardite Humic Acid: Microscopic Analysis of the Structure and Dynamics. Environmental Science & Technology. 51: 5414-5424. PMID 28440077 DOI: 10.1021/Acs.Est.7B00266  1
2017 Montero-Morales L, Maresch D, Castilho A, Turupcu A, Ilieva KM, Crescioli S, Karagiannis SN, Lupinek C, Oostenbrink C, Altmann F, Steinkellner H. Recombinant plant-derived human IgE glycoproteomics. Journal of Proteomics. 161: 81-87. PMID 28400175 DOI: 10.1016/J.Jprot.2017.04.002  1
2017 Grishkovskaya I, Paumann-Page M, Tscheliessnig R, Stampler J, Hofbauer S, Soudi M, Sevcnikar B, Oostenbrink C, Furtmüller PG, Djinović-Carugo K, Nauseef WM, Obinger C. Structure of human promyeloperoxidase (proMPO) and the role of the propeptide for processing and maturation. The Journal of Biological Chemistry. PMID 28348079 DOI: 10.1074/Jbc.M117.775031  1
2017 Margreitter C, Reif MM, Oostenbrink C. Update on phosphate and charged post-translationally modified amino acid parameters in the GROMOS force field. Journal of Computational Chemistry. 38: 714-720. PMID 28120339 DOI: 10.1002/Jcc.24733  1
2017 van Gunsteren WF, Daura X, Hansen N, Mark AE, Oostenbrink C, Riniker S, Smith LJ. Validierung von molekularen Simulationen: eine Übersicht verschiedener Aspekte Angewandte Chemie. 130: 894-915. DOI: 10.1002/Ange.201702945  1
2016 van Gunsteren WF, Allison JR, Daura X, Dolenc J, Hansen N, Mark AE, Oostenbrink C, Rusu VH, Smith LJ. Deriving Structural Information from Experimentally Measured Data on Biomolecules. Angewandte Chemie (International Ed. in English). PMID 27862777 DOI: 10.1002/Anie.201601828  1
2016 van Leeuwen J, Pons C, Mellor JC, Yamaguchi TN, Friesen H, Koschwanez J, Ušaj MM, Pechlaner M, Takar M, Ušaj M, VanderSluis B, Andrusiak K, Bansal P, Baryshnikova A, Boone CE, ... ... Oostenbrink C, et al. Exploring genetic suppression interactions on a global scale. Science (New York, N.Y.). 354. PMID 27811238 DOI: 10.1126/Science.Aag0839  1
2016 Graf MM, Maurer M, Oostenbrink C. Free-energy calculations of residue mutations in a tripeptide using various methods to overcome inefficient sampling. Journal of Computational Chemistry. PMID 27634475 DOI: 10.1002/Jcc.24488  1
2016 Hofbauer S, Dalla Sega M, Scheiblbrandner S, Jandova Z, Schaffner I, Mlynek G, Djinović-Carugo K, Battistuzzi G, Furtmüller PG, Oostenbrink C, Obinger C. Chemistry and Molecular Dynamics Simulations of Heme b-HemQ and Coproheme-HemQ. Biochemistry. 55: 5398-412. PMID 27599156 DOI: 10.1021/Acs.Biochem.6B00701  1
2016 Margreitter C, Oostenbrink C. Optimization of Protein Backbone Dihedral Angles by Means of Hamiltonian Reweighting. Journal of Chemical Information and Modeling. 56: 1823-34. PMID 27559757 DOI: 10.1021/Acs.Jcim.6B00399  1
2016 Ruiter Ad, Oostenbrink C. Extended Thermodynamic Integration: Efficient Prediction of Lambda Derivatives at Nonsimulated Points. Journal of Chemical Theory and Computation. 12: 4476-86. PMID 27494138 DOI: 10.1021/Acs.Jctc.6B00458  0.01
2016 Gasselhuber B, Graf MM, Jakopitsch C, Zamocky M, Nicolussi A, Furtmüller PG, Oostenbrink C, Carpena X, Obinger C. Interaction with the Redox Cofactor MYW and Functional Role of a Mobile Arginine in Eukaryotic Catalase-Peroxidase. Biochemistry. 55: 3528-41. PMID 27293030 DOI: 10.1021/Acs.Biochem.6B00436  1
2016 Maurer M, de Beer SB, Oostenbrink C. Calculation of Relative Binding Free Energy in the Water-Filled Active Site of Oligopeptide-Binding Protein A. Molecules (Basel, Switzerland). 21. PMID 27092480 DOI: 10.3390/Molecules21040499  1
2016 Margreitter C, Mayrhofer P, Kunert R, Oostenbrink C. Antibody humanization by molecular dynamics simulations-in-silico guided selection of critical backmutations. Journal of Molecular Recognition : Jmr. 29: 266-75. PMID 26748949 DOI: 10.1002/Jmr.2527  1
2016 Pechlaner M, Reif MM, Oostenbrink C. Reparametrisation of united-atom amine solvation in the GROMOS force field Molecular Physics. 115: 1144-1154. DOI: 10.1080/00268976.2016.1255797  0.01
2016 Olsen L, Jørgensen FS, Oostenbrink C. Cytochrome P450 Mediated Drug Metabolism Rsc Drug Discovery Series. 2016: 66-78. DOI: 10.1039/9781782622376-00066  1
2016 van Gunsteren WF, Allison JR, Daura X, Dolenc J, Hansen N, Mark AE, Oostenbrink C, Rusu VH, Smith LJ. Bestimmung von Strukturinformation aus experimentellen Messdaten für Biomoleküle Angewandte Chemie. 128: 16222-16244. DOI: 10.1002/Ange.201601828  1
2015 Pechlaner M, Oostenbrink C. Multiple Binding Poses in the Hydrophobic Cavity of Bee Odorant Binding Protein AmelOBP14. Journal of Chemical Information and Modeling. 55: 2633-43. PMID 26633245 DOI: 10.1021/Acs.Jcim.5B00673  1
2015 Sündermann A, Solc R, Tunega D, Haberhauer G, Gerzabek MH, Oostenbrink C. Vienna Soil-Organic-Matter Modeler--Generating condensed-phase models of humic substances. Journal of Molecular Graphics & Modelling. 62: 253-261. PMID 26521208 DOI: 10.1016/J.Jmgm.2015.10.007  1
2015 Gasselhuber B, Carpena X, Graf MM, Pirker KF, Nicolussi A, Sündermann A, Hofbauer S, Zamocky M, Furtmüller PG, Jakopitsch C, Oostenbrink C, Fita I, Obinger C. Eukaryotic Catalase-Peroxidase: The Role of the Trp-Tyr-Met Adduct in Protein Stability, Substrate Accessibility, and Catalysis of Hydrogen Peroxide Dismutation. Biochemistry. 54: 5425-38. PMID 26290940 DOI: 10.1021/Acs.Biochem.5B00831  1
2015 Graf MM, Sucharitakul J, Bren U, Chu DB, Koellensperger G, Hann S, Furtmüller PG, Obinger C, Peterbauer CK, Oostenbrink C, Chaiyen P, Haltrich D. Reaction of pyranose dehydrogenase from Agaricus meleagris with its carbohydrate substrates. The Febs Journal. 282: 4218-41. PMID 26284701 DOI: 10.1111/Febs.13417  1
2015 Reif MM, Oostenbrink C. Toward the correction of effective electrostatic forces in explicit-solvent molecular dynamics simulations: restraints on solvent-generated electrostatic potential and solvent polarization. Theoretical Chemistry Accounts. 134: 2. PMID 26097404 DOI: 10.1007/S00214-014-1600-8  1
2015 Castilho A, Gruber C, Thader A, Oostenbrink C, Pechlaner M, Steinkellner H, Altmann F. Processing of complex N-glycans in IgG Fc-region is affected by core fucosylation. Mabs. 7: 863-70. PMID 26067753 DOI: 10.1080/19420862.2015.1053683  1
2015 Olsen L, Oostenbrink C, Jørgensen FS. Prediction of cytochrome P450 mediated metabolism. Advanced Drug Delivery Reviews. 86: 61-71. PMID 25958010 DOI: 10.1016/J.Addr.2015.04.020  1
2015 Grandits M, Oostenbrink C. Selectivity of cytosolic phospholipase A2 type IV toward arachidonyl phospholipids. Journal of Molecular Recognition : Jmr. 28: 447-57. PMID 25703463 DOI: 10.1002/Jmr.2462  1
2015 Zolghadr B, Gasselhuber B, Windwarder M, Pabst M, Kracher D, Kerndl M, Zayni S, Hofinger-Horvath A, Ludwig R, Haltrich D, Oostenbrink C, Obinger C, Kosma P, Messner P, Schäffer C. UDP-sulfoquinovose formation by Sulfolobus acidocaldarius. Extremophiles : Life Under Extreme Conditions. 19: 451-67. PMID 25605538 DOI: 10.1007/S00792-015-0730-9  1
2015 Garate JA, Stöckl J, Fernández-Alonso Mdel C, Artner D, Haegman M, Oostenbrink C, Jiménez-Barbero J, Beyaert R, Heine H, Kosma P, Zamyatina A. Anti-endotoxic activity and structural basis for human MD-2·TLR4 antagonism of tetraacylated lipid A mimetics based on βGlcN(1↔1)αGlcN scaffold. Innate Immunity. 21: 490-503. PMID 25394365 DOI: 10.1177/1753425914550426  1
2015 Graf MMH, Zhixiong L, Bren U, Haltrich D, Gunsteren WFv, Oostenbrink C. Pyranose dehydrogenase ligand promiscuity Plos Computational Biology. DOI: 10.3929/Ethz-A-010346839  1
2015 Olsen L, Oostenbrink C, Jørgensen FS. Prediction of cytochrome P450 mediated metabolism Advanced Drug Delivery Reviews. 86: 61-71. DOI: 10.1016/j.addr.2015.04.020  1
2015 Zolghadr B, Gasselhuber B, Windwarder M, Pabst M, Kracher D, Kerndl M, Zayni S, Hofinger-Horvath A, Ludwig R, Haltrich D, Oostenbrink C, Obinger C, Kosma P, Messner P, Schäffer C. UDP-sulfoquinovose formation by Sulfolobus acidocaldarius Extremophiles. 19: 451-467. DOI: 10.1007/s00792-015-0730-9  1
2014 Graf MM, Zhixiong L, Bren U, Haltrich D, van Gunsteren WF, Oostenbrink C. Pyranose dehydrogenase ligand promiscuity: a generalized approach to simulate monosaccharide solvation, binding, and product formation. Plos Computational Biology. 10: e1003995. PMID 25500811 DOI: 10.1371/Journal.Pcbi.1003995  1
2014 Nørholm AB, Francotte P, Goffin E, Botez I, Danober L, Lestage P, Pirotte B, Kastrup JS, Olsen L, Oostenbrink C. 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. Journal of Chemical Information and Modeling. 54: 3404-16. PMID 25420075 DOI: 10.1021/Ci500559B  1
2014 Bren U, Fuchs JE, Oostenbrink C. Cooperative binding of aflatoxin B1 by cytochrome P450 3A4: a computational study. Chemical Research in Toxicology. 27: 2136-47. PMID 25398138 DOI: 10.1021/Tx5004062  1
2014 Reif MM, Oostenbrink C. Molecular dynamics simulation of configurational ensembles compatible with experimental FRET efficiency data through a restraint on instantaneous FRET efficiencies. Journal of Computational Chemistry. 35: 2319-32. PMID 25338770 DOI: 10.1002/Jcc.23756  1
2014 Grandits M, Oostenbrink C. Molecular dynamics simulations of the auxin-binding protein 1 in complex with indole-3-acetic acid and naphthalen-1-acetic acid. Proteins. 82: 2744-55. PMID 25043515 DOI: 10.1002/Prot.24639  1
2014 Sündermann A, Reif MM, Hofbauer S, Obinger C, Oostenbrink C. Investigation of ion binding in chlorite dismutases by means of molecular dynamics simulations. Biochemistry. 53: 4869-79. PMID 24988286 DOI: 10.1021/Bi500467H  1
2014 Traxlmayr MW, Lobner E, Hasenhindl C, Stadlmayr G, Oostenbrink C, Rüker F, Obinger C. Construction of pH-sensitive Her2-binding IgG1-Fc by directed evolution. Biotechnology Journal. 9: 1013-22. PMID 24964247 DOI: 10.1002/Biot.201300483  1
2014 Németh E, Schilli GK, Nagy G, Hasenhindl C, Gyurcsik B, Oostenbrink C. Design of a colicin E7 based chimeric zinc-finger nuclease. Journal of Computer-Aided Molecular Design. 28: 841-50. PMID 24952471 DOI: 10.1007/S10822-014-9765-8  1
2014 Hasenhindl C, Lai B, Delgado J, Traxlmayr MW, Stadlmayr G, Rüker F, Serrano L, Oostenbrink C, Obinger C. Creating stable stem regions for loop elongation in Fcabs - insights from combining yeast surface display, in silico loop reconstruction and molecular dynamics simulations. Biochimica Et Biophysica Acta. 1844: 1530-40. PMID 24792385 DOI: 10.1016/J.Bbapap.2014.04.020  1
2014 Hofbauer S, Gruber C, Pirker KF, Sündermann A, Schaffner I, Jakopitsch C, Oostenbrink C, Furtmüller PG, Obinger C. Transiently produced hypochlorite is responsible for the irreversible inhibition of chlorite dismutase. Biochemistry. 53: 3145-57. PMID 24754261 DOI: 10.1021/Bi500401K  1
2014 Loos A, Gruber C, Altmann F, Mehofer U, Hensel F, Grandits M, Oostenbrink C, Stadlmayr G, Furtmüller PG, Steinkellner H. Expression and glycoengineering of functionally active heteromultimeric IgM in plants. Proceedings of the National Academy of Sciences of the United States of America. 111: 6263-8. PMID 24706782 DOI: 10.1073/Pnas.1320544111  1
2014 Schwaighofer A, Pechlaner M, Oostenbrink C, Kotlowski C, Araman C, Mastrogiacomo R, Pelosi P, Knoll W, Nowak C, Larisika M. Insights into structural features determining odorant affinities to honey bee odorant binding protein 14. Biochemical and Biophysical Research Communications. 446: 1042-6. PMID 24661875 DOI: 10.1016/J.Bbrc.2014.03.054  1
2014 Lin Z, Oostenbrink C, van Gunsteren WF. 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. European Biophysics Journal : Ebj. 43: 113-9. PMID 24504380 DOI: 10.1007/S00249-014-0943-3  1
2014 Garate JA, Perez-Acle T, Oostenbrink C. On the thermodynamics of carbon nanotube single-file water loading: free energy, energy and entropy calculations. Physical Chemistry Chemical Physics : Pccp. 16: 5119-28. PMID 24477412 DOI: 10.1039/C3Cp54554G  1
2014 Lai B, Hasenhindl C, Obinger C, Oostenbrink C. Molecular dynamics simulation of the crystallizable fragment of IgG1-insights for the design of Fcabs. International Journal of Molecular Sciences. 15: 438-55. PMID 24451126 DOI: 10.3390/Ijms15010438  1
2014 Lai B, Nagy G, Garate JA, Oostenbrink C. Entropic and enthalpic contributions to stereospecific ligand binding from enhanced sampling methods. Journal of Chemical Information and Modeling. 54: 151-8. PMID 24372516 DOI: 10.1021/Ci4006657  1
2014 Nagy G, Oostenbrink C. Dihedral-based segment identification and classification of biopolymers I: proteins. Journal of Chemical Information and Modeling. 54: 266-77. PMID 24364820 DOI: 10.1021/Ci400541D  1
2014 Nagy G, Oostenbrink C. Dihedral-based segment identification and classification of biopolymers II: polynucleotides. Journal of Chemical Information and Modeling. 54: 278-88. PMID 24364355 DOI: 10.1021/Ci400542N  1
2014 Reif MM, Oostenbrink C. Net charge changes in the calculation of relative ligand-binding free energies via classical atomistic molecular dynamics simulation. Journal of Computational Chemistry. 35: 227-43. PMID 24249099 DOI: 10.1002/Jcc.23490  1
2013 de Ruiter A, Oostenbrink C. Protein-Ligand Binding from Distancefield Distances and Hamiltonian Replica Exchange Simulations. Journal of Chemical Theory and Computation. 9: 883-92. PMID 26588732 DOI: 10.1021/Ct300967A  1
2013 Perić-Hassler L, Stjernschantz E, Oostenbrink C, Geerke DP. CYP 2D6 binding affinity predictions using multiple ligand and protein conformations. International Journal of Molecular Sciences. 14: 24514-30. PMID 24351831 DOI: 10.3390/Ijms141224514  1
2013 Artner D, Oblak A, Ittig S, Garate JA, Horvat S, Arrieumerlou C, Hofinger A, Oostenbrink C, Jerala R, Kosma P, Zamyatina A. Conformationally constrained lipid A mimetics for exploration of structural basis of TLR4/MD-2 activation by lipopolysaccharide. Acs Chemical Biology. 8: 2423-32. PMID 23952219 DOI: 10.1021/Cb4003199  1
2013 Zou C, Larisika M, Nagy G, Srajer J, Oostenbrink C, Chen X, Knoll W, Liedberg B, Nowak C. 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. The Journal of Physical Chemistry. B. 117: 9606-14. PMID 23930980 DOI: 10.1021/Jp404573Q  1
2013 Grandits M, Michlmayr H, Sygmund C, Oostenbrink C. Calculation of substrate binding affinities for a bacterial GH78 rhamnosidase through molecular dynamics simulations. Journal of Molecular Catalysis. B, Enzymatic. 92: 34-43. PMID 23914137 DOI: 10.1016/J.Molcatb.2013.03.012  1
2013 Petrov D, Margreitter C, Grandits M, Oostenbrink C, Zagrovic B. A systematic framework for molecular dynamics simulations of protein post-translational modifications. Plos Computational Biology. 9: e1003154. PMID 23874192 DOI: 10.1371/Journal.Pcbi.1003154  1
2013 Sündermann A, Oostenbrink C. Molecular dynamics simulations give insight into the conformational change, complex formation, and electron transfer pathway for cytochrome P450 reductase. Protein Science : a Publication of the Protein Society. 22: 1183-95. PMID 23832577 DOI: 10.1002/Pro.2307  1
2013 Graf MM, Bren U, Haltrich D, Oostenbrink C. Molecular dynamics simulations give insight into D-glucose dioxidation at C2 and C3 by Agaricus meleagris pyranose dehydrogenase. Journal of Computer-Aided Molecular Design. 27: 295-304. PMID 23591812 DOI: 10.1007/S10822-013-9645-7  1
2013 Garate JA, Oostenbrink C. Free-energy differences between states with different conformational ensembles. Journal of Computational Chemistry. 34: 1398-408. PMID 23526629 DOI: 10.1002/Jcc.23276  1
2013 Reif MM, Winger M, Oostenbrink C. Testing of the GROMOS Force-Field Parameter Set 54A8: Structural Properties of Electrolyte Solutions, Lipid Bilayers, and Proteins. Journal of Chemical Theory and Computation. 9: 1247-1264. PMID 23418406 DOI: 10.1021/Ct300874C  1
2013 de Ruiter A, Boresch S, Oostenbrink C. Comparison of thermodynamic integration and Bennett acceptance ratio for calculating relative protein-ligand binding free energies. Journal of Computational Chemistry. 34: 1024-34. PMID 23335287 DOI: 10.1002/Jcc.23229  1
2013 Garate JA, Oostenbrink C. Lipid A from lipopolysaccharide recognition: structure, dynamics and cooperativity by molecular dynamics simulations. Proteins. 81: 658-74. PMID 23184816 DOI: 10.1002/Prot.24223  1
2012 Reif MM, Hünenberger PH, Oostenbrink C. New Interaction Parameters for Charged Amino Acid Side Chains in the GROMOS Force Field. Journal of Chemical Theory and Computation. 8: 3705-23. PMID 26593015 DOI: 10.1021/Ct300156H  1
2012 de Ruiter A, Oostenbrink C. Efficient and Accurate Free Energy Calculations on Trypsin Inhibitors. Journal of Chemical Theory and Computation. 8: 3686-95. PMID 26593013 DOI: 10.1021/Ct200750P  1
2012 Hofbauer S, Bellei M, Sündermann A, Pirker KF, Hagmüller A, Mlynek G, Kostan J, Daims H, Furtmüller PG, Djinović-Carugo K, Oostenbrink C, Battistuzzi G, Obinger C. Redox thermodynamics of high-spin and low-spin forms of chlorite dismutases with diverse subunit and oligomeric structures. Biochemistry. 51: 9501-12. PMID 23126649 DOI: 10.1021/Bi3013033  1
2012 Nagy G, Oostenbrink C. Rationalization of stereospecific binding of propranolol to cytochrome P450 2D6 by free energy calculations. European Biophysics Journal : Ebj. 41: 1065-76. PMID 23086294 DOI: 10.1007/S00249-012-0865-X  1
2012 Reif MM, Mach L, Oostenbrink C. Molecular insight into propeptide-protein interactions in cathepsins L and O. Biochemistry. 51: 8636-53. PMID 23009386 DOI: 10.1021/Bi300802A  1
2012 de Beer SB, Venkataraman H, Geerke DP, Oostenbrink C, Vermeulen NP. Free energy calculations give insight into the stereoselective hydroxylation of α-ionones by engineered cytochrome P450 BM3 mutants. Journal of Chemical Information and Modeling. 52: 2139-48. PMID 22765880 DOI: 10.1021/Ci300243N  1
2012 Bren U, Oostenbrink C. Cytochrome P450 3A4 inhibition by ketoconazole: tackling the problem of ligand cooperativity using molecular dynamics simulations and free-energy calculations. Journal of Chemical Information and Modeling. 52: 1573-82. PMID 22587011 DOI: 10.1021/Ci300118X  1
2012 Steiner D, Oostenbrink C, van Gunsteren WF. Calculation of the relative free energy of oxidation of Azurin at pH 5 and pH 9. Journal of Computational Chemistry. 33: 1467-77. PMID 22528559 DOI: 10.1002/Jcc.22972  1
2012 Gößler-Schöfberger R, Hesser G, Reif MM, Friedmann J, Duscher B, Toca-Herrera JL, Oostenbrink C, Jilek A. A stereochemical switch in the aDrs model system, a candidate for a functional amyloid. Archives of Biochemistry and Biophysics. 522: 100-6. PMID 22510364 DOI: 10.1016/J.Abb.2012.04.006  1
2012 Oostenbrink C, de Ruiter A, Hritz J, Vermeulen N. Malleability and versatility of cytochrome P450 active sites studied by molecular simulations. Current Drug Metabolism. 13: 190-6. PMID 22208533 DOI: 10.2174/138920012798918453  1
2012 Oostenbrink C. Free energy calculations from one-step perturbations. Methods in Molecular Biology (Clifton, N.J.). 819: 487-99. PMID 22183553 DOI: 10.1007/978-1-61779-465-0_28  0.01
2012 Lai B, Oostenbrink C. Binding free energy, energy and entropy calculations using simple model systems Theoretical Chemistry Accounts. 131: 1-13. DOI: 10.1007/S00214-012-1272-1  1
2011 Malde AK, Zuo L, Breeze M, Stroet M, Poger D, Nair PC, Oostenbrink C, Mark AE. An Automated Force Field Topology Builder (ATB) and Repository: Version 1.0. Journal of Chemical Theory and Computation. 7: 4026-37. PMID 26598349 DOI: 10.1021/Ct200196M  1
2011 Eichenberger AP, Allison JR, Dolenc J, Geerke DP, Horta BA, Meier K, Oostenbrink C, Schmid N, Steiner D, Wang D, van Gunsteren WF. GROMOS++ Software for the Analysis of Biomolecular Simulation Trajectories. Journal of Chemical Theory and Computation. 7: 3379-90. PMID 26598168 DOI: 10.1021/Ct2003622  1
2011 Riniker S, Christ CD, Hansen HS, Hünenberger PH, Oostenbrink C, Steiner D, van Gunsteren WF. Calculation of relative free energies for ligand-protein binding, solvation, and conformational transitions using the GROMOS software. The Journal of Physical Chemistry. B. 115: 13570-7. PMID 22039957 DOI: 10.1021/Jp204303A  1
2011 Lange JH, Venhorst J, van Dongen MJ, Frankena J, Bassissi F, de Bruin NM, den Besten C, de Beer SB, Oostenbrink C, Markova N, Kruse CG. Biophysical and physicochemical methods differentiate highly ligand-efficient human D-amino acid oxidase inhibitors. European Journal of Medicinal Chemistry. 46: 4808-19. PMID 21880399 DOI: 10.1016/J.Ejmech.2011.04.023  1
2011 de Ruiter A, Oostenbrink C. Free energy calculations of protein-ligand interactions. Current Opinion in Chemical Biology. 15: 547-52. PMID 21684797 DOI: 10.1016/J.Cbpa.2011.05.021  1
2011 Steiner D, Oostenbrink C, Diederich F, Zürcher M, van Gunsteren WF. Calculation of binding free energies of inhibitors to plasmepsin II. Journal of Computational Chemistry. 32: 1801-12. PMID 21488062 DOI: 10.1002/Jcc.21761  1
2011 De Beer SB, Glättli A, Hutzler J, Vermeulen NP, Oostenbrink C. Molecular dynamics simulations and free energy calculations on the enzyme 4-hydroxyphenylpyruvate dioxygenase. Journal of Computational Chemistry. 32: 2160-9. PMID 21484838 DOI: 10.1002/Jcc.21798  1
2011 de Ruiter A, Mader A, Kunert R, Oostenbrink C. Molecular Simulations to Rationalize Humanized Ab2/3H6 Activity Australian Journal of Chemistry. 64: 900. DOI: 10.1071/Ch10467  0.01
2011 Vasanthanathan P, Lastdrager J, Oostenbrink C, Commandeur JNM, Vermeulen NPE, Jørgensen FS, Olsen L. Identification of CYP1A2 ligands by structure-based and ligand-based virtual screening Medchemcomm. 2: 853-859. DOI: 10.1039/C1Md00087J  1
2011 Eichenberger AP, Allison JR, Dolenc J, Geerke DP, Horta BAC, Meier K, Oostenbrink C, Schmid N, Steiner D, Wang D, Van Gunsteren WF. GROMOS++ software for the analysis of biomolecular simulation trajectories Journal of Chemical Theory and Computation. 7: 3379-3390. DOI: 10.1021/ct2003622  1
2011 Malde AK, Zuo L, Breeze M, Stroet M, Poger D, Nair PC, Oostenbrink C, Mark AE. An Automated force field Topology Builder (ATB) and repository: Version 1.0 Journal of Chemical Theory and Computation. 7: 4026-4037. DOI: 10.1021/ct200196m  1
2011 Hritz J, Läppchen T, Oostenbrink C. Fast and Efficient Calculations of Binding Affinities for C8-Substituted GTP Analogues to the FtsZ Protein Biophysical Journal. 100: 158a-159a. DOI: 10.1016/J.Bpj.2010.12.1081  0.08
2010 Hritz J, Läppchen T, Oostenbrink C. Calculations of binding affinity between C8-substituted GTP analogs and the bacterial cell-division protein FtsZ. European Biophysics Journal : Ebj. 39: 1573-80. PMID 20559630 DOI: 10.1007/S00249-010-0614-Y  1
2010 Stjernschantz E, Oostenbrink C. Improved ligand-protein binding affinity predictions using multiple binding modes. Biophysical Journal. 98: 2682-91. PMID 20513413 DOI: 10.1016/J.Bpj.2010.02.034  1
2010 Vasanthanathan P, Olsen L, Jørgensen FS, Vermeulen NP, Oostenbrink C. Computational prediction of binding affinity for CYP1A2-ligand complexes using empirical free energy calculations. Drug Metabolism and Disposition: the Biological Fate of Chemicals. 38: 1347-54. PMID 20413725 DOI: 10.1124/Dmd.110.032946  1
2010 Stjernschantz E, Reinen J, Meinl W, George BJ, Glatt H, Vermeulen NP, Oostenbrink C. Comparison of murine and human estrogen sulfotransferase inhibition in vitro and in silico--implications for differences in activity, subunit dimerization and substrate inhibition. Molecular and Cellular Endocrinology. 317: 127-40. PMID 20025931 DOI: 10.1016/J.Mce.2009.12.001  1
2010 de Beer SB, Vermeulen NP, Oostenbrink C. The role of water molecules in computational drug design. Current Topics in Medicinal Chemistry. 10: 55-66. PMID 19929830 DOI: 10.2174/156802610790232288  1
2010 Santos R, Hritz J, Oostenbrink C. Role of water in molecular docking simulations of cytochrome P450 2D6. Journal of Chemical Information and Modeling. 50: 146-54. PMID 19899781 DOI: 10.1021/Ci900293E  1
2010 Venäläinen T, Molnár F, Oostenbrink C, Carlberg C, Peräkylä M. Molecular mechanism of allosteric communication in the human PPARalpha-RXRalpha heterodimer. Proteins. 78: 873-87. PMID 19847917 DOI: 10.1002/Prot.22613  1
2009 Rydberg P, Vasanthanathan P, Oostenbrink C, Olsen L. Fast prediction of cytochrome P450 mediated drug metabolism. Chemmedchem. 4: 2070-9. PMID 19852016 DOI: 10.1002/Cmdc.200900363  1
2009 Zoldák G, Aumüller T, Lücke C, Hritz J, Oostenbrink C, Fischer G, Schmid FX. A library of fluorescent peptides for exploring the substrate specificities of prolyl isomerases Biochemistry. 48: 10423-10436. PMID 19785464 DOI: 10.1021/Bi9014242  1
2009 Hritz J, Oostenbrink C. Efficient free energy calculations for compounds with multiple stable conformations separated by high energy barriers. The Journal of Physical Chemistry. B. 113: 12711-20. PMID 19722597 DOI: 10.1021/Jp902968M  1
2009 Vasanthanathan P, Hritz J, Taboureau O, Olsen L, Jørgensen FS, Vermeulen NP, Oostenbrink C. Virtual screening and prediction of site of metabolism for cytochrome P450 1A2 ligands. Journal of Chemical Information and Modeling. 49: 43-52. PMID 19099399 DOI: 10.1021/Ci800371F  1
2009 Vasanthanathan P, Taboureau O, Oostenbrink C, Vermeulen NP, Olsen L, Jørgensen FS. Classification of cytochrome P450 1A2 inhibitors and noninhibitors by machine learning techniques. Drug Metabolism and Disposition: the Biological Fate of Chemicals. 37: 658-64. PMID 19056915 DOI: 10.1124/Dmd.108.023507  1
2009 Oostenbrink C. Efficient free energy calculations on small molecule host-guest systems - a combined linear interaction energy/one-step perturbation approach. Journal of Computational Chemistry. 30: 212-21. PMID 18785242 DOI: 10.1002/Jcc.21116  0.01
2008 Hritz J, de Ruiter A, Oostenbrink C. Impact of plasticity and flexibility on docking results for cytochrome P450 2D6: a combined approach of molecular dynamics and ligand docking. Journal of Medicinal Chemistry. 51: 7469-77. PMID 18998665 DOI: 10.1021/Jm801005M  1
2008 Stjernschantz E, Vermeulen NP, Oostenbrink C. Computational prediction of drug binding and rationalisation of selectivity towards cytochromes P450. Expert Opinion On Drug Metabolism & Toxicology. 4: 513-27. PMID 18484912 DOI: 10.1517/17425255.4.5.513  1
2008 Hritz J, Oostenbrink C. Hamiltonian replica exchange molecular dynamics using soft-core interactions. The Journal of Chemical Physics. 128: 144121. PMID 18412437 DOI: 10.1063/1.2888998  1
2008 Stjernschantz E, van Vugt-Lussenburg BM, Bonifacio A, de Beer SB, van der Zwan G, Gooijer C, Commandeur JN, Vermeulen NP, Oostenbrink C. Structural rationalization of novel drug metabolizing mutants of cytochrome P450 BM3. Proteins. 71: 336-52. PMID 17957765 DOI: 10.1002/Prot.21697  1
2007 Hritz J, Oostenbrink C. Optimization of replica exchange molecular dynamics by fast mimicking. The Journal of Chemical Physics. 127: 204104. PMID 18052416 DOI: 10.1063/1.2790427  1
2007 de Graaf C, Oostenbrink C, Keizers PH, van Vugt-Lussenburg BM, Commandeur JN, Vermeulen NP. Free energies of binding of R- and S-propranolol to wild-type and F483A mutant cytochrome P450 2D6 from molecular dynamics simulations. European Biophysics Journal : Ebj. 36: 589-99. PMID 17333164 DOI: 10.1007/S00249-006-0126-Y  1
2007 de Graaf C, Oostenbrink C, Keizers PH, van Vugt-Lussenburg BM, van Waterschoot RA, Tschirret-Guth RA, Commandeur JN, Vermeulen NP. Molecular modeling-guided site-directed mutagenesis of cytochrome P450 2D6. Current Drug Metabolism. 8: 59-77. PMID 17266524 DOI: 10.2174/138920007779315062  1
2007 van Vugt-Lussenburg BM, Stjernschantz E, Lastdrager J, Oostenbrink C, Vermeulen NP, Commandeur JN. Identification of critical residues in novel drug metabolizing mutants of cytochrome P450 BM3 using random mutagenesis. Journal of Medicinal Chemistry. 50: 455-61. PMID 17266197 DOI: 10.1021/Jm0609061  1
2007 Keller B, Christen M, Oostenbrink C, van Gunsteren WF. On using oscillating time-dependent restraints in MD simulation Journal of Biomolecular Nmr. 37: 1-14. PMID 17180446 DOI: 10.1007/S10858-006-9081-2  1
2006 Stjernschantz E, Marelius J, Medina C, Jacobsson M, Vermeulen NP, Oostenbrink C. Are automated molecular dynamics simulations and binding free energy calculations realistic tools in lead optimization? An evaluation of the linear interaction energy (LIE) method. Journal of Chemical Information and Modeling. 46: 1972-83. PMID 16995728 DOI: 10.1021/Ci0601214  1
2006 van Gunsteren WF, Bakowies D, Baron R, Chandrasekhar I, Christen M, Daura X, Gee P, Geerke DP, Glättli A, Hünenberger PH, Kastenholz MA, Oostenbrink C, Schenk M, Trzesniak D, van der Vegt NF, et al. Biomolecular modeling: Goals, problems, perspectives. Angewandte Chemie (International Ed. in English). 45: 4064-92. PMID 16761306 DOI: 10.1002/Anie.200502655  1
2006 Dolenc J, Baron R, Oostenbrink C, Koller J, Van Gunsteren WF. Configurational entropy change of netropsin and distamycin upon DNA minor-groove binding Biophysical Journal. 91: 1460-1470. PMID 16731550 DOI: 10.1529/Biophysj.105.074617  1
2006 de Graaf C, Oostenbrink C, Keizers PH, van der Wijst T, Jongejan A, Vermeulen NP. Catalytic site prediction and virtual screening of cytochrome P450 2D6 substrates by consideration of water and rescoring in automated docking. Journal of Medicinal Chemistry. 49: 2417-30. PMID 16610785 DOI: 10.1021/Jm0508538  1
2006 Zhou Y, Oostenbrink C, Jongejan A, Van Gunsteren WF, Hagen WR, De Leeuw SW, Jongejan JA. 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. Journal of Computational Chemistry. 27: 857-67. PMID 16541426 DOI: 10.1002/Jcc.20378  1
2006 Stortelder A, Keizers PH, Oostenbrink C, De Graaf C, De Kruijf P, Vermeulen NP, Gooijer C, Commandeur JN, Van der Zwan G. Binding of 7-methoxy-4-(aminomethyl)-coumarin to wild-type and W128F mutant cytochrome P450 2D6 studied by time-resolved fluorescence spectroscopy. The Biochemical Journal. 393: 635-43. PMID 16190863 DOI: 10.1042/Bj20051169  1
2006 Oostenbrink C, Van Gunsteren WF. Calculating zeros: Non-equilibrium free energy calculations Chemical Physics. 323: 102-108. DOI: 10.1016/J.Chemphys.2005.08.054  1
2006 van Gunsteren WF, Bakowies D, Baron R, Chandrasekhar I, Christen M, Daura X, Gee P, Geerke DP, Glättli A, Hünenberger PH, Kastenholz MA, Oostenbrink C, Schenk M, Trzesniak D, van der Vegt NFA, et al. Biomolekulare Modellierung: Ziele, Probleme, Perspektiven Angewandte Chemie. 118: 4168-4198. DOI: 10.1002/Ange.200502655  1
2005 Oostenbrink C, van Gunsteren WF. Methane clustering in explicit water: effect of urea on hydrophobic interactions. Physical Chemistry Chemical Physics : Pccp. 7: 53-8. PMID 19785172 DOI: 10.1039/B413167C  1
2005 Christen M, Hünenberger PH, Bakowies D, Baron R, Bürgi R, Geerke DP, Heinz TN, Kastenholz MA, Kräutler V, Oostenbrink C, Peter C, Trzesniak D, van Gunsteren WF. The GROMOS software for biomolecular simulation: GROMOS05. Journal of Computational Chemistry. 26: 1719-51. PMID 16211540 DOI: 10.1002/Jcc.20303  1
2005 Keizers PH, de Graaf C, de Kanter FJ, Oostenbrink C, Feenstra KA, Commandeur JN, Vermeulen NP. Metabolic regio- and stereoselectivity of cytochrome P450 2D6 towards 3,4-methylenedioxy-N-alkylamphetamines: in silico predictions and experimental validation. Journal of Medicinal Chemistry. 48: 6117-27. PMID 16162012 DOI: 10.1021/Jm050338+  1
2005 Oostenbrink C, Juchli D, van Gunsteren WF. Amine hydration: a united-atom force-field solution. Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry. 6: 1800-4. PMID 16075431 DOI: 10.1002/Cphc.200400542  1
2005 Oostenbrink C, van Gunsteren WF. Efficient calculation of many stacking and pairing free energies in DNA from a few molecular dynamics simulations. Chemistry (Weinheim An Der Bergstrasse, Germany). 11: 4340-8. PMID 15880545 DOI: 10.1002/Chem.200401120  1
2005 Oostenbrink C, Soares TA, van der Vegt NF, van Gunsteren WF. Validation of the 53A6 GROMOS force field. European Biophysics Journal : Ebj. 34: 273-84. PMID 15803330 DOI: 10.1007/S00249-004-0448-6  1
2005 Soares TA, Hünenberger PH, Kastenholz MA, Kräutler V, Lenz T, Lins RD, Oostenbrink C, van Gunsteren WF. An improved nucleic acid parameter set for the GROMOS force field. Journal of Computational Chemistry. 26: 725-37. PMID 15770662 DOI: 10.1002/Jcc.20193  1
2005 Oostenbrink C, van Gunsteren WF. Free energies of ligand binding for structurally diverse compounds. Proceedings of the National Academy of Sciences of the United States of America. 102: 6750-4. PMID 15767587 DOI: 10.1073/Pnas.0407404102  1
2005 van den Bosch M, Swart M, Snijders JG, Berendsen HJ, Mark AE, Oostenbrink C, van Gunsteren WF, Canters GW. Calculation of the redox potential of the protein azurin and some mutants. Chembiochem : a European Journal of Chemical Biology. 6: 738-46. PMID 15747387 DOI: 10.1002/Cbic.200400244  1
2005 Dolenc J, Oostenbrink C, Koller J, van Gunsteren WF. Molecular dynamics simulations and free energy calculations of netropsin and distamycin binding to an AAAAA DNA binding site. Nucleic Acids Research. 33: 725-33. PMID 15687382 DOI: 10.1093/Nar/Gki195  1
2005 Soares TA, Daura X, Oostenbrink C, Smith LJ, van Gunsteren WF. Validation of the GROMOS force-field parameter set 45Alpha3 against nuclear magnetic resonance data of hen egg lysozyme. Journal of Biomolecular Nmr. 30: 407-22. PMID 15630561 DOI: 10.1007/S10858-004-5430-1  0.36
2005 Zhou Y, Oostenbrink C, Van Gunsteren WF, Hagen WR, De Leeuw SW, Jongejan JA. Relative stability of homochiral and heterochiral dialanine peptides. Effects of perturbation pathways and force-field parameters on free energy calculations Molecular Physics. 103: 1961-1969. DOI: 10.1080/00268970500096889  1
2004 Peter C, Oostenbrink C, van Dorp A, van Gunsteren WF. Estimating entropies from molecular dynamics simulations. The Journal of Chemical Physics. 120: 2652-61. PMID 15268408 DOI: 10.1063/1.1636153  1
2004 Oostenbrink C, Villa A, Mark AE, Van Gunsteren WF. A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6 Journal of Computational Chemistry. 25: 1656-1676. PMID 15264259 DOI: 10.1002/Jcc.20090  1
2004 Oostenbrink C, van Gunsteren WF. Free energies of binding of polychlorinated biphenyls to the estrogen receptor from a single simulation. Proteins. 54: 237-46. PMID 14696186 DOI: 10.1002/Prot.10558  1
2004 Glättli A, Oostenbrink C, Daura X, Geerke DP, Yu H, van Gunsteren WF. On the transferability of the SPC/L water model to biomolecular simulation Brazilian Journal of Physics. 34: 116-125. DOI: 10.1590/S0103-97332004000100015  0.2
2004 Chandrasekhar I, Oostenbrink C, van Gunsteren WF. Simulating the Physiological Phase of Hydrated DPPC Bilayers: The Ester Moiety Soft Materials. 2: 27-45. DOI: 10.1081/Smts-120030764  1
2004 Geerke DP, Oostenbrink C, van der Vegt NFA, van Gunsteren WF. An Effective Force Field for Molecular Dynamics Simulations of Dimethyl Sulfoxide and Dimethyl Sulfoxide−Water Mixtures The Journal of Physical Chemistry B. 108: 1436-1445. DOI: 10.1021/Jp035034I  1
2003 Oostenbrink C, van Gunsteren WF. Single-step perturbations to calculate free energy differences from unphysical reference states: limits on size, flexibility, and character. Journal of Computational Chemistry. 24: 1730-9. PMID 12964191 DOI: 10.1002/Jcc.10304  1
2003 Chandrasekhar I, Kastenholz M, Lins RD, Oostenbrink C, Schuler LD, Tieleman DP, van Gunsteren WF. A consistent potential energy parameter set for lipids: dipalmitoylphosphatidylcholine as a benchmark of the GROMOS96 45A3 force field. European Biophysics Journal : Ebj. 32: 67-77. PMID 12632209 DOI: 10.1007/S00249-002-0269-4  1
2002 Hansson T, Oostenbrink C, van Gunsteren W. Molecular dynamics simulations. Current Opinion in Structural Biology. 12: 190-6. PMID 11959496 DOI: 10.1016/S0959-440X(02)00308-1  0.2
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