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Search Items: Computer Simulation - , . hits: 35


** = Publications listed in SCI/SSCI - Journals (published in Web of Science)
* = peer-reviewed publication (not listed in SCI/SSCI)
Only: Full paper/article, Review, Proceedings Paper

2010

** Müllebner, A; Patel, A; Stamberg, W; Staniek, K; Rosenau, T; Netscher, T; Gille, L Modulation of the mitochondrial cytochrome bc1 complex activity by chromanols and related compounds..

Chem Res Toxicol. 2010; 23(1):193-202 WoS PubMed FullText FullText_BOKU

2009

** Hritz, J; Oostenbrink, C Efficient free energy calculations for compounds with multiple stable conformations separated by high energy barriers..

J Phys Chem B. 2009; 113(38):12711-12720 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

2008

** Chaix, R; Somel, M; Kreil, DP; Khaitovich, P; Lunter, GA Evolution of Primate Gene Expression: Drift and Corrective Sweeps?.

GENETICS. 2008; 180(3): 1379-1389. WoS PubMed PUBMED Central FullText FullText_BOKU

** 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..

J Med Chem. 2008; 51(23):7469-7477 WoS PubMed FullText FullText_BOKU

** Hritz, J; Oostenbrink, C Hamiltonian replica exchange molecular dynamics using soft-core interactions..

J Chem Phys. 2008; 128(14):144121-144121 WoS PubMed FullText FullText_BOKU

** Orlandini, S; Nejedlik, P; Eitzinger, J; Alexandrov, V; Toulios, L; Calanca, P; Trnka, M; Olesen, JE Impacts of climate change and variability on European agriculture: results of inventory analysis in COST 734 countries..

Ann N Y Acad Sci. 2008; 1146:338-353 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

2007

** Hritz, J; Oostenbrink, C Optimization of replica exchange molecular dynamics by fast mimicking..

J Chem Phys. 2007; 127(20):204104-204104 WoS PubMed FullText FullText_BOKU

** Keller, B; Christen, M; Oostenbrink, C; van Gunsteren, WF On using oscillating time-dependent restraints in MD simulation..

J Biomol NMR. 2007; 37(1):1-14 WoS PubMed FullText FullText_BOKU

** Matulla, C; Schmutz, S; Melcher, A; Gerersdorfer, T; Haas, P Assessing the impact of a downscaled climate change simulation on the fish fauna in an Inner-Alpine River..

Int J Biometeorol. 2007; 52(2):127-137 WoS PubMed FullText FullText_BOKU

** Peh, WY; Reimhult, E; Teh, HF; Thomsen, JS; Su, X Understanding ligand binding effects on the conformation of estrogen receptor alpha-DNA complexes: a combinational quartz crystal microbalance with dissipation and surface plasmon resonance study..

Biophys J. 2007; 92(12):4415-4423 WoS PubMed PUBMED Central FullText FullText_BOKU

** Standler, A; Koellensperger, G; Buchberger, W; Stingeder, G; Hann, S Determination of chloroplatinates by CE coupled to inductively coupled plasma sector field MS..

Electrophoresis. 2007; 28(19):3492-3499 WoS PubMed FullText FullText_BOKU

2006

** Dolenc, J; Baron, R; Oostenbrink, C; Koller, J; van Gunsteren, WF Configurational entropy change of netropsin and distamycin upon DNA minor-groove binding..

Biophys J. 2006; 91(4):1460-1470 WoS PubMed PUBMED Central FullText FullText_BOKU

** 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..

Biochem J. 2006; 393(Pt 3):635-643 WoS PubMed PUBMED Central FullText FullText_BOKU

** 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; Yu, HB Biomolecular modeling: Goals, problems, perspectives..

Angew Chem Int Ed Engl. 2006; 45(25):4064-4092 WoS PubMed FullText FullText_BOKU

** 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..

J Comput Chem. 2006; 27(7):857-867 WoS PubMed FullText FullText_BOKU

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..

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

** Deverall, MA; Gindl, E; Sinner, EK; Besir, H; Ruehe, J; Saxton, MJ; Naumann, CA Membrane lateral mobility obstructed by polymer-tethered lipids studied at the single molecule level..

Biophys J. 2005; 88(3):1875-1886 WoS PubMed PUBMED Central FullText FullText_BOKU

** 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 Res. 2005; 33(2):725-733 WoS PubMed PUBMED Central 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 Methane clustering in explicit water: effect of urea on hydrophobic interactions..

Phys Chem Chem Phys. 2005; 7(1):53-58 WoS PubMed FullText FullText_BOKU

** Pietsch, SA; Hausenauer, H Using ergodic theory to assess the performance of ecosystem models..

Tree Physiol. 2005; 25(7):825-837 WoS PubMed FullText FullText_BOKU

** Seidl, R; Lexer, MJ; Jäger, D; Hönninger, K Evaluating the accuracy and generality of a hybrid patch model..

Tree Physiol. 2005; 25(7):939-951 WoS PubMed

** 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

** 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

2004

** Dimitrievski, K; Reimhult, E; Kasemo, B; Zhdanov, VP Simulations of temperature dependence of the formation of a supported lipid bilayer via vesicle adsorption..

Colloids Surf B Biointerfaces. 2004; 39(1-2):77-86 WoS PubMed FullText FullText_BOKU

** Kreil, DP; Karp, NA; Lilley, KS DNA microarray normalization methods can remove bias from differential protein expression analysis of 2D difference gel electrophoresis results..

Bioinformatics. 2004; 20(13):2026-2034 WoS PubMed 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

** 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..

J Comput Chem. 2004; 25(13):1656-1676 WoS PubMed FullText FullText_BOKU

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..

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

* Keckes, J; Burgert, I; Frühmann, K; Müller, M; Kölln, K; Hamilton, M; Burghammer, M; Roth, SV; Stanzl-Tschegg, S; Fratzl, P (2003): Cell-wall recovery after irreversible deformation of wood..

Nat Mater. 2003; 2(12):810-814 PubMed FullText FullText_BOKU

2002

** Fowler, S.B., Best, R., Toca-Herrera, J.L., Rutherford, T.J., Steward, A., Paci, E., Karplus, M., Clarke, J. Mechanical unfolding of a titin Ig domain: (1) Structure of unfolding intermediate revealed by combining AFM, molecular dynamic simulations, NMR and protein engineering.

J. Mol. Biol., 322, 841-849 WoS PubMed

** Hansson, T; Oostenbrink, C; van Gunsteren, W Molecular dynamics simulations..

Curr Opin Struct Biol. 2002; 12(2):190-196 WoS PubMed

** Rencurosi, A; Röhrling, J; Pauli, J; Potthast, A; Jäger, C; Pérez, S; Kosma, P; Imberty, A Polymorphism in the crystal structure of the cellulose fragment analogue methyl 4-O-methyl-beta-D-glucopyranosyl-(1-4)-beta-D-glucopyranoside..

Angew Chem Int Ed Engl. 2002; 41(22):4277-4281 WoS PubMed FullText FullText_BOKU

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