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Personal profile

Ancillary activities

  • StickyBits Creatives | Amersfoort | Directeur/eigenaar | 2018-05-01 - present

Ancillary activities are updated daily

Research

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. Marc obtained his PhD degree in 2010, on the topic of protein-DNA interaction modelling using molecular simulation techniques. Thereafter, he has been involved in various research projects as post-doctoral researcher at the Cambridge University (UK), Utrecht University and VU University Amsterdam where he currently holds a Senior Scientist position. His research focuses on the study of biomolecular interactions using computational molecular modeling and simulation techniques. Marc is currently involved in the Dutch e-Science center project “Enhancing protein-Drug binding prediction” where he is involved in method development for accurate protein-drug binding affinity prediction using free-energy methods. Part of this project is the MDStudio software platform for microservice based molecular dynamics workflows where Marc is project coordinator and lead developer.

Education/Academic qualification

PhD, Universiteit Utrecht

Oct 2005Feb 2010

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Free energy Chemical Compounds
Proteins Medicine & Life Sciences
Ligands Engineering & Materials Science
Benchmarking Medicine & Life Sciences
Drug Design Medicine & Life Sciences
DNA Medicine & Life Sciences
Sirtuin 1 Chemical Compounds
Molecular dynamics Chemical Compounds

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Research Output 2006 2019

  • 23 Article
  • 3 PhD Thesis - Research VU, graduation VU

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

Drug toxicity profiling of a Saccharomyces cerevisiae deubiquitinase deletion panel shows that acetaminophen mimics tyrosine

Huseinovic, A., van Dijk, M., Vermeulen, N. P. E., van Leeuwen, F., Kooter, J. M. & Vos, J. C., Mar 2018, In : Toxicology in Vitro. 47, p. 259-268 10 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Acetaminophen
Drug-Related Side Effects and Adverse Reactions
Yeast
Toxicity
Saccharomyces cerevisiae

Inter-individual variability in activity of the major drug metabolizing enzymes in liver homogenates of 20 Individuals

den Braver-Sewradj, S. P., den Braver, M. W., van Dijk, M., Zhang, Y., Dekker, S. J., Wijaya, L., Vermeulen, N. P. E., Richert, L., Commandeur, J. N. M. & Vos, J. C., 8 Jan 2018, In : Current Drug Metabolism. 19, 4, p. 370-381 12 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Liver
Glucuronosyltransferase
Oxidoreductases
Cytochromes
Glutathione Transferase
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