Total 13 results found.
Tag: Biomolecular simulation and modeling Ordering

Position: PhD student

Room: P2.75BTel: +31 20 59 87612Email:

Stephanie de Beer, PhD

Position: PhD student

Room: P2.75Tel: +31 20 5987608Email:


Position: Post-doc

Room: P2.75Tel: +31 20 59 87607 Email:


Position: Post-doc

Room: P2.75BTel: +31 20 59 83852Email:


Dr. Marc van Dijk

Position: Post-doc

Dr. Marc van Dijk studied Biology at Utrecht University and obtained his Master’s degree in Biomolecular Sciences and specialization in structural biology in 2005. Subsequently, he performed his PhD research at the NMR Department of the Bijvoet Center for structural biology at Utrecht University. Van Dijk obtained his PhD degree in 2010, on the topic of protein-DNA interaction modelling using molecular simulation techniques.

Thereafter, Van Dijk has been involved in various research projects as post-doctoral researcher at the Cambridge University (UK), Utrecht University and VU University Amsterdam. His research focuses on the study of molecular interactions using computational structural techniques.

In addition, he has a strong interest in making the academic computational toolkit available to the broader audience as user friendly (online) software. He acquired broad experience in this field through the projects he worked for in the role of scientific programmer, web developer and interface designer. Moreover, he is the owner of StickyBits creatives, a company that designs and develops for the digital world with special interest in education and science.

Room: P2.75BTel: +31 20 59 87612Email:


Position: Post-doc

Room: P2.75ATel: +31 20 59 87607Email:


Dr. Chris Oostenbrink

Position: Assistant Professor

Chris Oostenbrink studied both Chemistry and Pharmacochemistry at the Vrije Universiteit, Amsterdam. He graduated twice in 2000 with specialisations in Theoretical Chemistry and Computational Medicinal Chemistry, in both cases cum laude. In 2004 he obtained his PhD at the Swiss Federal Institute of Technology (ETH) in Zurich, Switzerland, in the group of prof. W.F. van Gunsteren on the calculation of (binding) free energies in biomolecular simulations. In October 2004, he was appointed Assistent professor Computational Medicinal Chemistry and Toxicology (CMCT) at the VU. In 2005 he received two ‘young talent’ grants, a Bioinformatics Breakthrough grant from NWO-Horizon, and a VENI-grant from NWO-CW. In his work he is aiming to inter-connect computational and experimental approaches to study biomolecular systems and to show that computational tools studying protein structure and dynamics and protein-ligand interactions are complementary to experiments. Since 2009, Chris Oostenbrink has been appointed group leader in Molecular Modeling and Simulation at BOKU University, Vienna, and part-time as assistant-professor within the Division of Molecular and Computational Toxicology. See also his personal website.

Room: P2.62Tel: +31 20 5987606Email:

Dr. Daan Geerke

Position: Assistant Professor

In 2007, Daan Geerke obtained his PhD degree 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 of Prof. Dr. Nico P.E. Vermeulen at VU University. 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.

Room: O|2 03E11Tel: +31 20 59 87606Email:

Prof.dr. Nico Vermeulen

Position: Head of Division of Molecular Toxicology

Professor Vermeulen graduated in Chemistry in 1975 at the Catholic University of Nijmegen. In 1980 he obtained his PhD in Pharmacology from the University of Leiden. In 1985 he was appointed professor of Molecular Toxicology at the Vrije Universiteit, Amsterdam.

Amongst others he is organizer of the yearly (Dutch) Post-academic Course on General Toxicology, the yearly international LACDR/EUFEPS course on High-Throughput Drug Metabolism and Disposition and of the PharmSciFair 2005 in Nice, a member of the Committee for the Registration of Toxicologists, chairman of the Section Pharmacochemistry of the Royal Netherlands Chemical Society (KNCV), a member of the Future Strategies Committee of the KNCV and councillor of the European Society of Biochemical Pharmacology (ESBP). In 2012 he chaired the first Joint MDO/European ISSX Meeting in Noordwijk, The Netherlands.

He was/is President-elect (2000-2001), President (2002-2003), Past-president (2004-2005) and Honorary Life-time member of the International Society for the Study of Xenobiotics (ISSX). In 2006, he received the European ISSX Scientific Achievement Award, and in 2011 an Honorary Doctorate from the University of Copenhagen.

Professor Vermeulen is on the editorial boards of the journals Biomarkers, Biomedical & Environmental Sciences, Biochemical Pharmacology, Chemico-Biological Interactions, Chirality, Chemistry & Biodiversity, Chemical Research in Toxicology, Drug Metabolism Reviews, Expert Opinions in Drug Metabolism & Toxicology, Toxicology and Xenobiotica. He is associate editor of Current Drug Metabolism/Drug Metabolism Letters and editor of Environmental Toxicology & Pharmacology.

Work of him and his group is since 2001 taken up in the ISI-list of Highly Cited Researchers.


Room: P2.22Tel: +31 20 5987590Email:

CV [pdf]

QM/MM-Based Fitting of Atomic Polarizabilities for Use in Condensed-Phase Biomolecular Simulation Vosmeer CR, Rustenburg AS,  Rice JE, Horn HW, Swope WC, Geerke DP J. Chem. Theory Comput. 2012 DOI: 10.1021/ct300085z

Cytochrome P450 3A4 Inhibition by Ketoconazole: Tackling the Problem of Ligand Cooperativity Using Molecular Dynamics Simulations and Free-Energy Calculations Bren U, Oostenbrink BC J. Chem. Inf. Model., 2012, 52, 1573-1582 DOI:10.1021/ci300118x

Regio- and Stereoselective Hydroxylation of Optically Active α-Ionone Enantiomers by Engineered Cytochrome P450 BM3 Mutants Harini Venkataraman, Stephanie B. A. de Beer, Daan P. Geerke, Nico P. E. Vermeulen, Jan N. M. Commandeur Advanced Synthesis & Catalysis, Volume 354, Issue 11-12, pages 2172–2184, August 13, 2012

Free Energy Calculations Give Insight into the Stereoselective Hydroxylation of α-Ionones by Engineered Cytochrome P450 BM3 Mutants; Stephanie B.A. de Beer, Harini Venkataraman, Daan P. Geerke, Chris Oostenbrink, Nico P.E. Vermeulen; J. Chem. Inf. Model., 2012, 52 (8), pp 2139–2148; DOI: 10.1021/ci300243n