Publications | In press |
| 70. |
M. Reif, P. Hünenberger and C. Oostenbrink New interaction parameters for charged amino acid side chains in the GROMOS force field J. Chem. Theory Comp. (2012) online 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. (2012) online 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. (2012) online 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. (2012) online doi: 10.1021/ct200750p |
| 66. |
C. Oostenbrink, A. de Ruiter, J. Hritz and N.P.E. Vermeulen Malleability and versatility of Cytochrome P450 active sites studied by molecular simulations Curr. Drug Metab. 13 (2012) 190 - 196 |
| 65. |
C. Oostenbrink Free energy calculations from one-step perturbations In: "Computational drug discovery and design" (Methods in Molecular Biology 819), R. Baron, Ed., Humana Press, New York (2012) |
| 64. |
A.K. Malde, L. Zuo, M. Breeze, M. Stroet, D. Poger, P.C. Nair, C. Oostenbrink, A.E. Mark An automated force field topology builder (ATB) and repository: version 1.0 J. Chem. Theor. Comput. 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. Sjernschantz, 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 towards 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 |
Publications in press | published |