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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 Conference contribution
  • 1 PhD Thesis - Research VU, graduation VU

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

Luirink, R. A., Dekker, S. J., Capoferri, L., Kuiper, C. L., Janssen, L. F. H., Ari, M. E., Vermeulen, N. P. E., Vos, J. C., Commandeur, J. N. M. & Geerke, D. P., Jul 2018, In : Journal of Inorganic Biochemistry. 184, p. 115-122 8 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Floxacillin
Hydroxylation
Cytochrome P-450 Enzyme System
Metabolites
Enzymes

Multiple-choice knapsack for assigning partial atomic charges in drug-like molecules

Engler, M. S., Caron, B., Veen, L., Geerke, D. P., Mark, A. E. & Klau, G. W., Aug 2018, 18th International Workshop on Algorithms in Bioinformatics, WABI 2018. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, Vol. 113, p. 1-13 13 p. 16

Research output: Chapter in Book / Report / Conference proceedingConference contributionAcademicpeer-review

Molecules
Atoms
Dynamic programming
Linear programming
Polynomials

A Systematic Approach to Calibrate a Transferable Polarizable Force Field Parameter Set for Primary Alcohols

Visscher, K. M., Vosmeer, C. R., Luirink, R. A. & Geerke, D. P., Mar 2017, In : Journal of Computational Chemistry. 38, 8, p. 508-517

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Free energy
free energy
Ligands
Drug Design
Molecular Dynamics Simulation

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

van Dijk, M., Ter Laak, A. M., Wichard, J. D., Capoferri, L., Vermeulen, N. P. E. & Geerke, D. P., 25 Sep 2017, In : Journal of Chemical Information and Modeling. 57, 9, p. 2294-2308 15 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Aromatase Inhibitors
Cytochrome P-450 Enzyme System
energy
interaction
workflow