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Personal information

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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Cytochrome P-450 Enzyme System Chemical Compounds
Hydroxylation Chemical Compounds
Molecular dynamics Chemical Compounds
Free energy Chemical Compounds
Ligands Engineering & Materials Science
Molecules Engineering & Materials Science
Norisoprenoids Chemical Compounds
affinity Physics & Astronomy

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Research Output 2003 2019

  • 53 Article
  • 3 PhD Thesis - Research VU, graduation VU
  • 1 Conference contribution

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

Rifai, E. A., van Dijk, M., Vermeulen, N. P. E., Yanuar, A. & Geerke, D. P., 11 Sep 2019, In : Journal of Chemical Information and Modeling. p. 4018-4033 16 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Sirtuin 1
Molecular mechanics
mechanic
Free energy
Ligands

Applicability and performance of linear interaction energy based binding affinity calculation

Rifai, E. A., 2019, 183 p.

Research output: PhD ThesisPhD Thesis - Research VU, graduation VUAcademic

Open Access
File

Automated partial atomic charge assignment for drug-like molecules: A fast knapsack approach

Engler, M. S., Caron, B., Veen, L., Geerke, D. P., Mark, A. E. & Klau, G. W., 5 Feb 2019, In : Algorithms for Molecular Biology. 14, 1, p. 1-10 10 p., 1.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Knapsack
Drugs
Assignment
Charge
Molecules

Deriving Force-Field Parameters from First Principles Using a Polarizable and Higher Order Dispersion Model

Visscher, K. M. & Geerke, D. P., 14 Feb 2019, In : Journal of Chemical Theory and Computation. 15, 3, p. 1875–1883 9 p.

Research output: Contribution to JournalArticleAcademicpeer-review

field theory (physics)
inclusions
Molecular mechanics
Alkanes
Dipole moment

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

Frydenvang, K., Verkade-Vreeker, M. C. A., Dohmen, F., Commandeur, J. N. M., Rafiq, M., Mirza, O., Jørgensen, F. S. & Geerke, D. P., 1 May 2019, In : PLoS ONE. 14, 5, e0217292.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
dithiothreitol
Dithiothreitol
cytochrome P-450
Structural analysis
Cytochrome P-450 Enzyme System