Geerke DP - Search Results

1

Combined Simulation and Mutation Studies to Elucidate Selectivity of Unsubstituted Amphetamine-like Cathinones at the Dopamine Transporter.

Seddik A, Geerke DP, Stockner T, Holy M, Kudlacek O, Cozzi NV, Ruoho AE, Sitte HH, Ecker GF. Seddik A, et al. Among authors: geerke dp. Mol Inform. 2017 May;36(5-6). doi: 10.1002/minf.201600094. Epub 2016 Nov 8. Mol Inform. 2017. PMID: 27860344

2

CYP 2D6 binding affinity predictions using multiple ligand and protein conformations.

Perić-Hassler L, Stjernschantz E, Oostenbrink C, Geerke DP. Perić-Hassler L, et al. Among authors: geerke dp. Int J Mol Sci. 2013 Dec 17;14(12):24514-30. doi: 10.3390/ijms141224514. Int J Mol Sci. 2013. PMID: 24351831 Free PMC article.

3

Integrative Modeling Strategies for Predicting Drug Toxicities at the eTOX Project.

Sanz F, Carrió P, López O, Capoferri L, Kooi DP, Vermeulen NP, Geerke DP, Montanari F, Ecker GF, Schwab CH, Kleinöder T, Magdziarz T, Pastor M. Sanz F, et al. Among authors: geerke dp. Mol Inform. 2015 Jun;34(6-7):477-84. doi: 10.1002/minf.201400193. Epub 2015 Jun 11. Mol Inform. 2015. PMID: 27490391

4

The role of protein plasticity in computational rationalization studies on regioselectivity in testosterone hydroxylation by cytochrome P450 BM3 mutants.

de Beer SB, van Bergen LA, Keijzer K, Rea V, Venkataraman H, Guerra CF, Bickelhaupt FM, Vermeulen NP, Commandeur JN, Geerke DP. de Beer SB, et al. Among authors: geerke dp. Curr Drug Metab. 2012 Feb;13(2):155-66. doi: 10.2174/138920012798918471. Curr Drug Metab. 2012. PMID: 22208530

5

Free energy calculations give insight into the stereoselective hydroxylation of α-ionones by engineered cytochrome P450 BM3 mutants.

de Beer SB, Venkataraman H, Geerke DP, Oostenbrink C, Vermeulen NP. de Beer SB, et al. Among authors: geerke dp. J Chem Inf Model. 2012 Aug 27;52(8):2139-48. doi: 10.1021/ci300243n. Epub 2012 Jul 19. J Chem Inf Model. 2012. PMID: 22765880

6

Towards automated binding affinity prediction using an iterative linear interaction energy approach.

Vosmeer CR, Pool R, Van Stee MF, Peric-Hassler L, Vermeulen NP, Geerke DP. Vosmeer CR, et al. Among authors: geerke dp. Int J Mol Sci. 2014 Jan 9;15(1):798-816. doi: 10.3390/ijms15010798. Int J Mol Sci. 2014. PMID: 24413750 Free PMC article.

7

Linear Interaction Energy Based Prediction of Cytochrome P450 1A2 Binding Affinities with Reliability Estimation.

Capoferri L, Verkade-Vreeker MC, Buitenhuis D, Commandeur JN, Pastor M, Vermeulen NP, Geerke DP. Capoferri L, et al. Among authors: geerke dp. PLoS One. 2015 Nov 9;10(11):e0142232. doi: 10.1371/journal.pone.0142232. eCollection 2015. PLoS One. 2015. PMID: 26551865 Free PMC article.

8

Insights into regioselective metabolism of mefenamic acid by cytochrome P450 BM3 mutants through crystallography, docking, molecular dynamics, and free energy calculations.

Capoferri L, Leth R, ter Haar E, Mohanty AK, Grootenhuis PD, Vottero E, Commandeur JN, Vermeulen NP, Jørgensen FS, Olsen L, Geerke DP. Capoferri L, et al. Among authors: geerke dp. Proteins. 2016 Mar;84(3):383-96. doi: 10.1002/prot.24985. Epub 2016 Feb 3. Proteins. 2016. PMID: 26757175

9

Comprehensive and Automated Linear Interaction Energy Based Binding-Affinity Prediction for Multifarious Cytochrome P450 Aromatase Inhibitors.

van Dijk M, Ter Laak AM, Wichard JD, Capoferri L, Vermeulen NPE, Geerke DP. van Dijk M, et al. Among authors: geerke dp. J Chem Inf Model. 2017 Sep 25;57(9):2294-2308. doi: 10.1021/acs.jcim.7b00222. Epub 2017 Aug 23. J Chem Inf Model. 2017. PMID: 28776988 Free PMC article.

10

Binding free energy predictions of farnesoid X receptor (FXR) agonists using a linear interaction energy (LIE) approach with reliability estimation: application to the D3R Grand Challenge 2.

Rifai EA, van Dijk M, Vermeulen NPE, Geerke DP. Rifai EA, et al. Among authors: geerke dp. J Comput Aided Mol Des. 2018 Jan;32(1):239-249. doi: 10.1007/s10822-017-0055-0. Epub 2017 Sep 9. J Comput Aided Mol Des. 2018. PMID: 28889350 Free PMC article.

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