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Daan Geerke obtained his PhD degree in 2007 within the Laboratory for Physical Chemistry at the ETH Zürich, under supervision of Prof. Dr. Wilfred F. van Gunsteren. Afterwards he joined the research group of Dr. Julia E. Rice and Dr. William C. Swope at the IBM Almaden Research Center in San Jose, California, for a postdoctoral fellowship. In 2009 Daan Geerke has been appointed Assistant-Professor within the MCT research group headed by Prof. Dr. Nico P.E. Vermeulen and (since 2017) Prof. Dr. Paul Jennings at Vrije Universiteit. Currently, he is supervising a senior scientist and three PhD students, and he lectures a variety of bachelor and master courses in the fields of computational chemistry, (bio-)molecular modeling, structural biology and (statistical) thermodynamics. His research focuses on in silico rationalization and prediction of drug metabolism and action upon binding to flexible enzymes such as human and bacterial Cytochrome P450s, proteases or methyl transferases, in direct collaboration with ‘wet-chemistry’ colleagues within MCT,/VU, medical centers and industry. In addition he has since many years worked on development of biomolecular force fields and on inclusion of quantum and electronic polarization effects in simulation. He has published more than 40 scientific publications within these research fields. In 2009, he has been awarded a NWO-Veni grant, in 2013, he has been awarded a NWO-Vidi grant, in 2015 a NWO / NLeSC eScience grant (together with prof. Gunnar Klau / CWI) and since 2016 several HPC grants from the VU High Performance Computing council. In addition, he has been coordinator of the scientific activities at VU University in the context of the IMI-JU eTOX project on in silico prediction of toxicities.

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Research Output 2003 2018

  • 48 Article
  • 1 PhD Thesis - Research VU, graduation VU
Floxacillin
Hydroxylation
Cytochrome P-450 Enzyme System
Metabolites
Enzymes
Open Access
Free energy
free energy
Ligands
Drug Design
Molecular Dynamics Simulation
Open Access
Aromatase Inhibitors
Cytochrome P-450 Enzyme System
energy
interaction
workflow

Engineered factor Xa variants retain procoagulant activity independent of direct factor Xa inhibitors

Verhoef, D., Visscher, K. M., Vosmeer, C. R., Cheung, K. L., Reitsma, P. H., Geerke, D. P. & Bos, M. H. A. 13 Sep 2017 In : Nature Communications. 8, 1, p. 528

Research output: Contribution to journalArticle

Open Access
Factor Xa
inhibitors
Coagulation
Blood Coagulation Factor Inhibitors
Anticoagulants