BOKU - Universität für Bodenkultur Wien - Forschungsinformationssystem

Logo BOKU-Forschungsportal


Suchbegriffe: Molecular dynamics, . Treffer: 68

** = Publikationen gelistet in SCI/SSCI (veröffentlicht im Web of Science)
* = Publikationen in sonstigen peer-reviewten Journalen (ggf. noch nicht im WoS veröffentlicht)
Filter: Originalarbeit, Übersichtsarbeit, Konferenzband Originalarbeit


** Roither, B; Oostenbrink, C; Pfeiler, G; Koelbl, H; Schreiner, W Pembrolizumab Induces an Unexpected Conformational Change in the CC '-loop of PD-1.

CANCERS. 2021; 13(1), 5 WoS PubMed FullText FullText_BOKU

** van Gunsteren, WF; Daura, X; Fuchs, PFJ; Hansen, N; Horta, BAC; Hunenberger, 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. 2021; 22(3): 264-282. WoS PubMed FullText FullText_BOKU


** Diem, M; Oostenbrink, C; The effect of different cutoff schemes in molecular simulations of proteins..

J Comput Chem. 2020; 41(32):2740-2749 WoS PubMed FullText FullText_BOKU

** Grancic, P; Tunega, D Geometry and molecular arrangement of phosphatidylcholine-montmorillonite bioclays via classical molecular dynamics simulation.

APPL CLAY SCI. 2020; 198, 105815 WoS FullText FullText_BOKU

** Ohlknecht, C; Lier, B; Petrov, D; Fuch, J; Oostenbrink, C Correcting electrostatic artifacts due to net-charge changes in the calculation of ligand binding free energies.

J COMPUT CHEM. 2020; 41(10): 986-999. WoS PubMed FullText FullText_BOKU

** 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.

EUR J SOIL SCI. 2020; 71(5): 831-844. WoS PubMed FullText FullText_BOKU

** 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. 2020; 21, 557 WoS PubMed FullText FullText_BOKU

** Tunega, D; Gerzabek, MH; Haberhauer, G; Lischka, H; Solc, R; Aquino, AJA Adsorption process of polar and nonpolar compounds in a nanopore model of humic substances.

EUR J SOIL SCI. 2020; 71(5): 845-855. WoS FullText FullText_BOKU

** 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. 2020; 88(1):82-93 WoS PubMed FullText FullText_BOKU


** Jandova, Z; Jespers, W; Sotelo, E; Gutierrez-de-Teran, H; Oostenbrink, C Free-Energy Calculations for Bioisosteric Modifications of A(3) Adenosine Receptor Antagonists.

INT J MOL SCI. 2019; 20(14), 3499 WoS PubMed FullText FullText_BOKU

** Pfanzagl, V; Bellei, M; Hofbauer, S; Laurent, CVFP; Furtmüller, PG; Oostenbrink, C; Battistuzzi, G; Obinger, C; Redox thermodynamics of B-class dye-decolorizing peroxidases..

J Inorg Biochem. 2019; 199:110761 WoS PubMed FullText FullText_BOKU

** Turupcu, A; Blaukopf, M; Kosma, P; Oostenbrink, C; Molecular Conformations of Di-, Tri-, and Tetra-.

Int J Mol Sci. 2019; 21(1): WoS PubMed PUBMED Central FullText FullText_BOKU

** 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. 2019; 20(11):1527-1537 WoS PubMed PUBMED Central FullText FullText_BOKU


** Bakaric, D; Petrov, D; Mouvenchery, YK; Heissler, 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.

CHEM PHYS LIPIDS. 2018; 210: 38-46. WoS PubMed FullText FullText_BOKU

** Jandova, Z; Trosanova, Z; Weisova, V; Oostenbrink, C; Hritz, J Free energy calculations on the stability of the 14-3-3 zeta protein.

BBA-PROTEINS PROTEOM. 2018; 1866(3): 442-450. WoS PubMed FullText FullText_BOKU

** Maurer, M; Hansen, N; Oostenbrink, C Comparison of free-energy methods using a tripeptide-water model system.

J COMPUT CHEM. 2018; 39(26): 2226-2242. WoS PubMed FullText FullText_BOKU

** 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 Eng Des Sel. 2018; 31(7-8):257-265 WoS PubMed FullText FullText_BOKU

** van Gunsteren, WF; Daura, X; Hansen, N; Mark, AE; Oostenbrink, C; Riniker, S; Smith, LJ Validation of Molecular Simulation: An Overview of Issues.

ANGEW CHEM INT EDIT. 2018; 57(4): 884-902. WoS PubMed FullText FullText_BOKU


** Margreitter, C; Reif, MM; Oostenbrink, C Update on Phosphate and Charged Post-Translationally Modified Amino Acid Parameters in the GROMOS Force Field.

J COMPUT CHEM. 2017; 38(10): 714-720. WoS PubMed FullText FullText_BOKU

** Wozniak-Knopp, G; Stadlmayr, G; Perthold, JW; Stadlbauer, K; Woisetschlager, M; Sun, HJ; Ruker, F Designing Fcabs: well-expressed and stable high affinity antigen-binding Fc fragments.

PROTEIN ENG DES SEL. 2017; 30(9): 657-671. WoS PubMed FullText FullText_BOKU


** Margreitter, C; Mayrhofer, P; Kunert, R; Oostenbrink, C Antibody humanization by molecular dynamics simulations-in-silico guided selection of critical backmutations.

J MOL RECOGNIT. 2016; 29(6): 266-275. WoS PubMed FullText FullText_BOKU

** Maurer, M; de Beer, SBA; Oostenbrink, C Calculation of Relative Binding Free Energy in the Water-Filled Active Site of Oligopeptide-Binding Protein.

MOLECULES. 2016; 21(4): WoS FullText FullText_BOKU

** Schampera, B; Solc, R; Tunega, D; Dultz, S Experimental and molecular dynamics study on anion diffusion in organically modified bentonite.

APPL CLAY SCI. 2016; 120: 91-100. WoS FullText FullText_BOKU


** Garate, JA; Stöckl, J; Del Carmen Fernández-Alonso, M; 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 Immun. 2015; 21(5):490-503 WoS PubMed PUBMED Central FullText FullText_BOKU

** Graf, MMH; Sucharitakul, J; Bren, U; Chu, DB; Koellensperger, G; Hann, S; Furtmuller, PG; Obinger, C; Peterbauer, CK; Oostenbrink, C; Chaiyen, P; Haltrich, D Reaction of pyranose dehydrogenase from Agaricusmeleagris with its carbohydrate substrates.

FEBS J. 2015; 282(21): 4218-4241. WoS PubMed FullText FullText_BOKU

** Grandits, M; Oostenbrink, C Selectivity of cytosolic phospholipase A2 type IV toward arachidonyl phospholipids.

J MOL RECOGNIT. 2015; 28(7): 447-457. WoS PubMed FullText FullText_BOKU

** Olsen, L; Oostenbrink, C; Jorgensen, FS Prediction of cytochrome P450 mediated metabolism.

ADV DRUG DELIVER REV. 2015; 86: 61-71. WoS PubMed FullText FullText_BOKU

** 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.

THEOR CHEM ACC. 2015; 134(2): WoS FullText FullText_BOKU

** Schampera, B; Solc, R; Woche, SK; Mikutta, R; Dultz, S; Guggenberger, G; Tunega, D Surface structure of organoclays as examined by X-ray photoelectron spectroscopy and molecular dynamics simulations.

CLAY MINER. 2015; 50(3): 353-367. WoS FullText FullText_BOKU

** Solc, R; Tunega, D; Gerzabek, MH; Woche, SK; Bachmann, J Wettability of organically coated tridymite surface - molecular dynamics study.

PURE APPL CHEM. 2015; 87(4): 405-413. WoS FullText FullText_BOKU

** Sündermann, A; Solc, R; Tunega, D; Haberhauer, G; Gerzabek, MH; Oostenbrink, C; Vienna Soil-Organic-Matter Modeler-Generating condensed-phase models of humic substances..

J Mol Graph Model. 2015; 62:253-261 WoS PubMed FullText FullText_BOKU


** 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..

Biochim Biophys Acta. 2014; 1844(9):1530-1540 WoS PubMed PUBMED Central FullText FullText_BOKU

** Lai, B; Hasenhindl, C; Obinger, C; Oostenbrink, C Molecular Dynamics Simulation of the Crystallizable Fragment of IgG1-Insights for the Design of Fcabs.

INT J MOL SCI. 2014; 15(1): 438-455. WoS FullText FullText_BOKU

** Lin, ZX; 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.

EUR BIOPHYS J BIOPHY. 2014; 43(2-3): 113-119. WoS FullText FullText_BOKU

** Lotfi, A; Vrabec, J; Fischer, J Evaporation from a free liquid surface.

INT J HEAT MASS TRAN. 2014; 73: 303-317. WoS FullText FullText_BOKU

** Reif, MM; Oostenbrink, C Molecular Dynamics Simulation of Configurational Ensembles Compatible with Experimental FRET Efficiency Data Through a Restraint on Instantaneous FRET Efficiencies.

J COMPUT CHEM. 2014; 35(32): 2319-2332. WoS PubMed FullText FullText_BOKU

** Reif, MM; Oostenbrink, C Net charge changes in the calculation of relative ligand-binding free energies via classical atomistic molecular dynamics simulation..

J Comput Chem. 2014; 35(3):227-243 WoS PubMed PUBMED Central FullText FullText_BOKU

** 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.

BIOCHEM BIOPH RES CO. 2014; 446(4): 1042-1046. WoS FullText FullText_BOKU

** Udommaneethanakit, T; Rungrotmongkol, T; Frecer, V; Seneci, P; Miertus, S; Bren, U Drugs against avian influenza a virus: design of novel sulfonate inhibitors of neuraminidase n1..

Curr Pharm Des. 2014; 20(21):3478-3487 WoS PubMed


** de Ruiter, A; Boresch, S; Oostenbrink, C; Comparison of thermodynamic integration and Bennett acceptance ratio for calculating relative protein-ligand binding free energies..

J Comput Chem. 2013; 34(12):1024-1034 WoS PubMed FullText FullText_BOKU

** Sundermann, A; Oostenbrink, C Molecular dynamics simulations give insight into the conformational change, complex formation, and electron transfer pathway for cytochrome P450 reductase.

PROTEIN SCI. 2013; 22(9): 1183-1195. WoS FullText FullText_BOKU

** Uto, T; Hosoya, T; Hayashi, S; Yui, T Partial crystalline transformation of solvated cellulose IIII crystals, reproduced by theoretical calculations.

CELLULOSE. 2013; 20(2): 605-612. WoS FullText FullText_BOKU


** Oostenbrink, C; de Ruiter, A; Hritz, J; Vermeulen, N; Malleability and versatility of cytochrome P450 active sites studied by molecular simulations..

Curr Drug Metab. 2012; 13(2):190-196 WoS PubMed

** Steiner, D; Oostenbrink, C; van Gunsteren, WF Calculation of the relative free energy of oxidation of azurin at pH 5 and pH 9.

J COMPUT CHEM. 2012; 33(17): 1467-1477. WoS PubMed FullText FullText_BOKU


** De Beer, SBA; Glattli, A; Hutzler, J; Vermeulen, NPE; Oostenbrink, C Molecular Dynamics Simulations and Free Energy Calculations on the Enzyme 4-Hydroxyphenylpyruvate Dioxygenase.

J COMPUT CHEM. 2011; 32(10): 2160-2169. WoS FullText FullText_BOKU

** 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..

Eur J Med Chem. 2011; 46(10):4808-4819 WoS PubMed FullText FullText_BOKU

** Solc, R; Gerzabek, MH; Lischka, H; Tunega, D Wettability of kaolinite (001) surfaces - Molecular dynamic study.

GEODERMA. 2011; 169: 47-54. WoS FullText FullText_BOKU

** Steiner, D; Oostenbrink, C; Diederich, F; Zurcher, M; van Gunsteren, WF Calculation of Binding Free Energies of Inhibitors to Plasmepsin II.

J COMPUT CHEM. 2011; 32(9): 1801-1812. WoS PubMed


** Pasalic, H; Aquino, AJ; Tunega, D; Haberhauer, G; Gerzabek, MH; Georg, HC; Moraes, TF; Coutinho, K; Canuto, S; Lischka, H Thermodynamic stability of hydrogen-bonded systems in polar and nonpolar environments..

J Comput Chem. 2010; 31(10):2046-2055 WoS PubMed FullText FullText_BOKU


** Oostenbrink, C Efficient free energy calculations on small molecule host-guest systems - a combined linear interaction energy/one-step perturbation approach..

J Comput Chem. 2009; 30(2):212-221 WoS PubMed FullText FullText_BOKU


** 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. 2008; 71(1):336-352 WoS PubMed FullText FullText_BOKU

** Stjernschantz, E; Vermeulen, NP; Oostenbrink, C Computational prediction of drug binding and rationalisation of selectivity towards cytochromes P450..

Expert Opin Drug Metab Toxicol. 2008; 4(5):513-527 WoS PubMed FullText FullText_BOKU


** Sumardiono, S; Fischer, J Molecular simulations of droplet evaporation by heat transfer.

MICROFLUID NANOFLUID. 2007; 3(2): 127-140. WoS FullText FullText_BOKU


** 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..

J Comput Chem. 2005; 26(16):1719-1751 WoS PubMed FullText FullText_BOKU

** Oostenbrink, C; Juchli, D; van Gunsteren, WF Amine hydration: a united-atom force-field solution..

Chemphyschem. 2005; 6(9):1800-1804 WoS PubMed FullText FullText_BOKU

** Oostenbrink, C; Soares, TA; van der Vegt, NF; van Gunsteren, WF Validation of the 53A6 GROMOS force field..

Eur Biophys J. 2005; 34(4):273-284 WoS PubMed FullText FullText_BOKU

** Oostenbrink, C; van Gunsteren, WF Free energies of ligand binding for structurally diverse compounds..

Proc Natl Acad Sci U S A. 2005; 102(19):6750-6754 WoS PubMed PUBMED Central FullText FullText_BOKU

** 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..

J Comput Chem. 2005; 26(7):725-737 WoS PubMed FullText FullText_BOKU

** Tscheliessnig, R., Billes, W., Wendland, M., Fischer, J., Kolafa, J. Adsorption of benzene from an aqueous solution.

Molecular Simulation, 31, 9, 661; ISSN 0892-7022 WoS FullText FullText_BOKU

** 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. 2005; 6(4):738-746 WoS PubMed FullText FullText_BOKU


** Chandrasekhar, I; Oostenbrink, C; van Gunsteren, WF Simulating the physiological phase of hydrated DPPC bilayers: The ester moiety.

SOFT MATER. 2004; 2(1): 27-45. WoS FullText FullText_BOKU

** Oostenbrink, C; van Gunsteren, WF Free energies of binding of polychlorinated biphenyls to the estrogen receptor from a single simulation..

Proteins. 2004; 54(2):237-246 WoS PubMed FullText FullText_BOKU


** 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..

Eur Biophys J. 2003; 32(1):67-77 WoS PubMed FullText FullText_BOKU

** Oostenbrink, C; van Gunsteren, WF Single-step perturbations to calculate free energy differences from unphysical reference states: limits on size, flexibility, and character..

J Comput Chem. 2003; 24(14):1730-1739 WoS PubMed FullText FullText_BOKU


** Lishchuk, S.V., Fischer, J. Velocity distribution of water molecule in pores under microwave electric field..

Int. J. Thermal Sciences, 40, 717-723 WoS FullText FullText_BOKU

** Stoll, J., Vrabec, H., Hasse, H., Fischer, J. Comprehensive study of the vapour-liquid equilibria of the pure two-centre Lennard-Jones plus point quadrupole fluid..

Fluid Phase Equilibria, 179, 339-362 WoS FullText FullText_BOKU

** van Gunsteren, W; Bakowies, D; Burgi, R; Chandrasekhar, I; Christen, M; Daura, X; Gee, P; Glattli, A; Hansson, T; Oostenbrink, C; Peter, C; Pitera, J; Schuler, L; Soares, T; Yu, HB Molecular dynamics simulation of biomolecular systems.

CHIMIA. 2001; 55(10): 856-860. WoS


** Kriebel, C; Muller, A; Mecke, M; Winkelmann, J; Fischer, J Prediction of thermodynamic properties for fluid nitrogen with molecular dynamics simulations.

INT J THERMOPHYS. 1996; 17(6): 1349-1363. WoS FullText FullText_BOKU

© BOKU Wien Impressum