Geerke DP - Search Results

1

An anti-tuberculosis compound screen using a zebrafish infection model identifies an aspartyl-tRNA synthetase inhibitor.

Habjan E, Ho VQT, Gallant J, van Stempvoort G, Jim KK, Kuijl C, Geerke DP, Bitter W, Speer A. Habjan E, et al. Among authors: geerke dp. Dis Model Mech. 2021 Dec 1;14(12):dmm049145. doi: 10.1242/dmm.049145. Epub 2021 Dec 23. Dis Model Mech. 2021. PMID: 34643222 Free PMC article.

2

Engineering a self-sufficient Mycobacterium tuberculosis CYP130 by gene fusion with the reductase-domain of CYP102A1 from Bacillus megaterium.

Ortega Ugalde S, Luirink RA, Geerke DP, Vermeulen NPE, Bitter W, Commandeur JNM. Ortega Ugalde S, et al. Among authors: geerke dp. J Inorg Biochem. 2018 Mar;180:47-53. doi: 10.1016/j.jinorgbio.2017.12.003. Epub 2017 Dec 7. J Inorg Biochem. 2018. PMID: 29232638

3

Covalent Proteomimetic Inhibitor of the Bacterial FtsQB Divisome Complex.

Paulussen FM, Schouten GK, Moertl C, Verheul J, Hoekstra I, Koningstein GM, Hutchins GH, Alkir A, Luirink RA, Geerke DP, van Ulsen P, den Blaauwen T, Luirink J, Grossmann TN. Paulussen FM, et al. Among authors: geerke dp. J Am Chem Soc. 2022 Aug 24;144(33):15303-15313. doi: 10.1021/jacs.2c06304. Epub 2022 Aug 9. J Am Chem Soc. 2022. PMID: 35945166 Free PMC article.

4

Structural analysis of Cytochrome P450 BM3 mutant M11 in complex with dithiothreitol.

Frydenvang K, Verkade-Vreeker MCA, Dohmen F, Commandeur JNM, Rafiq M, Mirza O, Jørgensen FS, Geerke DP. Frydenvang K, et al. Among authors: geerke dp. PLoS One. 2019 May 24;14(5):e0217292. doi: 10.1371/journal.pone.0217292. eCollection 2019. PLoS One. 2019. PMID: 31125381 Free PMC article.

5

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

6

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.

7

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.

8

A combined computational and experimental study on selective flucloxacillin hydroxylation by cytochrome P450 BM3 variants.

Luirink RA, Dekker SJ, Capoferri L, Janssen LFH, Kuiper CL, Ari ME, Vermeulen NPE, Vos JC, Commandeur JNM, Geerke DP. Luirink RA, et al. Among authors: geerke dp. J Inorg Biochem. 2018 Jul;184:115-122. doi: 10.1016/j.jinorgbio.2018.04.013. Epub 2018 Apr 24. J Inorg Biochem. 2018. PMID: 29723739

9

A dominant activating RAC2 variant associated with immunodeficiency and pulmonary disease.

Smits BM, Lelieveld PHC, Ververs FA, Turkenburg M, de Koning C, van Dijk M, Leavis HL, Boelens JJ, Lindemans CA, Bloem AC, van de Corput L, van Montfrans J, Nierkens S, van Gijn ME, Geerke DP, Waterham HR, Koenderman L, Boes M. Smits BM, et al. Among authors: geerke dp. Clin Immunol. 2020 Mar;212:108248. doi: 10.1016/j.clim.2019.108248. Epub 2019 Aug 2. Clin Immunol. 2020. PMID: 31382036 No abstract available.

10

A Comparative Linear Interaction Energy and MM/PBSA Study on SIRT1-Ligand Binding Free Energy Calculation.

Rifai EA, van Dijk M, Vermeulen NPE, Yanuar A, Geerke DP. Rifai EA, et al. Among authors: geerke dp. J Chem Inf Model. 2019 Sep 23;59(9):4018-4033. doi: 10.1021/acs.jcim.9b00609. Epub 2019 Sep 11. J Chem Inf Model. 2019. PMID: 31461271 Free PMC article.

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