Oostenbrink C - Search Results

1

Calculation of relative free energies for ligand-protein binding, solvation, and conformational transitions using the GROMOS software.

Riniker S, Christ CD, Hansen HS, Hünenberger PH, Oostenbrink C, Steiner D, van Gunsteren WF. Riniker S, et al. Among authors: oostenbrink c. J Phys Chem B. 2011 Nov 24;115(46):13570-7. doi: 10.1021/jp204303a. Epub 2011 Nov 1. J Phys Chem B. 2011. PMID: 22039957

2

A consistent potential energy parameter set for lipids: dipalmitoylphosphatidylcholine as a benchmark of the GROMOS96 45A3 force field.

Chandrasekhar I, Kastenholz M, Lins RD, Oostenbrink C, Schuler LD, Tieleman DP, van Gunsteren WF. Chandrasekhar I, et al. Among authors: oostenbrink c. Eur Biophys J. 2003 Mar;32(1):67-77. doi: 10.1007/s00249-002-0269-4. Epub 2003 Jan 21. Eur Biophys J. 2003. PMID: 12632209

3

Single-step perturbations to calculate free energy differences from unphysical reference states: limits on size, flexibility, and character.

Oostenbrink C, van Gunsteren WF. Oostenbrink C, et al. J Comput Chem. 2003 Nov 15;24(14):1730-9. doi: 10.1002/jcc.10304. J Comput Chem. 2003. PMID: 12964191

4

Free energies of binding of polychlorinated biphenyls to the estrogen receptor from a single simulation.

Oostenbrink C, van Gunsteren WF. Oostenbrink C, et al. Proteins. 2004 Feb 1;54(2):237-46. doi: 10.1002/prot.10558. Proteins. 2004. PMID: 14696186

5

A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6.

Oostenbrink C, Villa A, Mark AE, van Gunsteren WF. Oostenbrink C, et al. J Comput Chem. 2004 Oct;25(13):1656-76. doi: 10.1002/jcc.20090. J Comput Chem. 2004. PMID: 15264259

6

Estimating entropies from molecular dynamics simulations.

Peter C, Oostenbrink C, van Dorp A, van Gunsteren WF. Peter C, et al. Among authors: oostenbrink c. J Chem Phys. 2004 Feb 8;120(6):2652-61. doi: 10.1063/1.1636153. J Chem Phys. 2004. PMID: 15268408

7

Validation of the GROMOS force-field parameter set 45Alpha3 against nuclear magnetic resonance data of hen egg lysozyme.

Soares TA, Daura X, Oostenbrink C, Smith LJ, van Gunsteren WF. Soares TA, et al. Among authors: oostenbrink c. J Biomol NMR. 2004 Dec;30(4):407-22. doi: 10.1007/s10858-004-5430-1. J Biomol NMR. 2004. PMID: 15630561

8

Molecular dynamics simulations and free energy calculations of netropsin and distamycin binding to an AAAAA DNA binding site.

Dolenc J, Oostenbrink C, Koller J, van Gunsteren WF. Dolenc J, et al. Among authors: oostenbrink c. Nucleic Acids Res. 2005 Feb 1;33(2):725-33. doi: 10.1093/nar/gki195. Print 2005. Nucleic Acids Res. 2005. PMID: 15687382 Free PMC article.

9

Calculation of the redox potential of the protein azurin and some mutants.

van den Bosch M, Swart M, Snijders JG, Berendsen HJ, Mark AE, Oostenbrink C, van Gunsteren WF, Canters GW. van den Bosch M, et al. Among authors: oostenbrink c. Chembiochem. 2005 Apr;6(4):738-46. doi: 10.1002/cbic.200400244. Chembiochem. 2005. PMID: 15747387

10

Free energies of ligand binding for structurally diverse compounds.

Oostenbrink C, van Gunsteren WF. Oostenbrink C, et al. Proc Natl Acad Sci U S A. 2005 May 10;102(19):6750-4. doi: 10.1073/pnas.0407404102. Epub 2005 Mar 14. Proc Natl Acad Sci U S A. 2005. PMID: 15767587 Free PMC article.

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