If you made any changes in Pure these will be visible here soon.

Research Output 2006 2018

  • 22 Article
  • 3 PhD Thesis - Research VU, graduation VU
Filter
Article
2018

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

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

Research output: Contribution to JournalArticleAcademicpeer-review

Liver
Glucuronosyltransferase
Oxidoreductases
Cytochromes
Glutathione Transferase
2017
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

eTOX ALLIES: an automated pipeLine for linear interaction energy-based simulations

Capoferri, C. L., van Dijk, M., Rustenburg, A. S., Wassenaar, T., Kooi, D. P., Rifai, E. A., Vermeulen, N. P. E. & Geerke, D. P., 2017, In : Journal of Cheminformatics. 9, 58, p. 1-13 13 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Pipelines
Ligands
energy
ligands
Free energy

Sense and simplicity in HADDOCK scoring: Lessons from CASP-CAPRI round 1

Vangone, A., Rodrigues, J. P. G. L. M., Xue, L. C., van Zundert, G. C. P., Geng, C., Kurkcuoglu, Z., Nellen, M., Narasimhan, S., Karaca, E., van Dijk, M., Melquiond, A. S. J., Visscher, K. M., Trellet, M., Kastritis, P. L. & Bonvin, A. M. J. J., Mar 2017, In : Proteins. 85, 3, p. 417-423 7 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Computational Biology
Static Electricity
Publications
Proteins
Servers
2016

The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes

van Zundert, G. C. P., Rodrigues, J. P. G. L. M., Trellet, M., Schmitz, C., Kastritis, P. L., Karaca, E., Melquiond, A. S. J., van Dijk, M., de Vries, S. J. & Bonvin, A. M. J. J., 22 Feb 2016, In : Journal of Molecular Biology. 428, 4, p. 720-5 6 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Drug Design
2014

Blind prediction of interfacial water positions in CAPRI

Lensink, M. F. , Moal, I. H. , Bates, P. A. , Kastritis, P. L. , Melquiond, A. S. J. , Karaca, E. , Schmitz, C. , van Dijk, M. , Bonvin, A. M. J. J. , Eisenstein, M. , Jiménez-García, B. , Grosdidier, S. , Solernou, A. , Pérez-Cano, L. , Pallara, C. , Fernández-Recio, J. , Xu, J. , Muthu, P. , Praneeth Kilambi, K. , Gray, J. J. & 38 others Grudinin, S., Derevyanko, G., Mitchell, J. C., Wieting, J., Kanamori, E., Tsuchiya, Y., Murakami, Y., Sarmiento, J., Standley, D. M., Shirota, M., Kinoshita, K., Nakamura, H., Chavent, M., Ritchie, D. W., Park, H., Ko, J., Lee, H., Seok, C., Shen, Y., Kozakov, D., Vajda, S., Kundrotas, P. J., Vakser, I. A., Pierce, B. G., Hwang, H., Vreven, T., Weng, Z., Buch, I., Farkash, E., Wolfson, H. J., Zacharias, M., Qin, S., Zhou, H-X., Huang, S-Y., Zou, X., Wojdyla, J. A., Kleanthous, C. & Wodak, S. J., Apr 2014, In : Proteins. 82, 4, p. 620-32 13 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Water
Proteins
Colicins
Molecular mechanics
Deoxyribonucleases

Mass spec studio for integrative structural biology

Rey, M., Sarpe, V., Burns, K. M., Buse, J., Baker, C. A. H., van Dijk, M., Wordeman, L., Bonvin, A. M. J. J. & Schriemer, D. C., 2014, In : Structure. 22, 10, p. 1538-48 11 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Tandem Mass Spectrometry
Mass Spectrometry
Deuterium
Information Storage and Retrieval
Structural Models
2013

Defining the limits of homology modeling in information-driven protein docking

Rodrigues, J. P. G. L. M., Melquiond, A. S. J., Karaca, E., Trellet, M., van Dijk, M., van Zundert, G. C. P., Schmitz, C., de Vries, S. J., Bordogna, A., Bonati, L. H., Kastritis, P. L. & Bonvin, A. M. J. J., Dec 2013, In : Proteins. 81, 12, p. 2119-2128

Research output: Contribution to JournalArticleAcademicpeer-review

Solvated protein-DNA docking using HADDOCK

van Dijk, M., Visscher, K. M., Bonvin, A. M. J. J. & Kastritis, P. L., 2013, In : Journal of Biomolecular NMR. 56, 1, p. 51-63 13 p.

Research output: Contribution to JournalArticleAcademicpeer-review

DNA
Benchmarking
Proteins
Water
Molecules
2012

A Flexible, Grid-Enabled Web Portal for GROMACS Molecular Dynamics Simulations

van Dijk, M., Wassenaar, T. A. & Bonvin, A. M. J. J., 2012, In : Journal of Chemical Theory and Computation. 8, 10, p. 3463-72 10 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Molecular dynamics
grids
molecular dynamics
Computer simulation
Molecular interactions

Rapid prediction of multi-dimensional NMR data sets

Gradmann, S., Ader, C., Heinrich, I., Nand, D., Dittmann, M., Cukkemane, A., van Dijk, M., Bonvin, A. M. J. J., Engelhard, M. & Baldus, M., Dec 2012, In : Journal of Biomolecular NMR. 54, 4, p. 377-387

Research output: Contribution to JournalArticleAcademicpeer-review

The structure of the XPF-ssDNA complex underscores the distinct roles of the XPF and ERCC1 helix- hairpin-helix domains in ss/ds DNA recognition

Das, D., Folkers, G., van Dijk, M., Jaspers, N. G. J., Hoeijmakers, J. H. J., Kaptein, R. & Boelens, R., 4 Apr 2012, In : Structure. 20, 4, p. 667-75 9 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Single-Stranded DNA Breaks
Deoxyribonuclease I
DNA
Guanine
DNA Repair

WeNMR: Structural Biology on the Grid

Wassenaar, T. A. , van Dijk, M. , Loureiro-Ferreira, N. , van der Schot, G. , de Vries, S. J. , Schmitz, C. , van der Zwan, J. , Boelens, R. , Giachetti, A. , Ferella, L. , Rosato, A. , Bertini, I. , Herrmann, T. , Jonker, H. R. A. , Bagaria, A. , Jaravine, V. , Guntert, P. , Schwalbe, H. , Vranken, W. F. , Doreleijers, J. F. & 16 others Vriend, G., Vuister, G. W., Franke, D., Kikhney, A., Svergun, D. I., Fogh, R. H., Ionides, J., Laue, E. D., Spronk, C., Jurksa, S., Verlato, M., Badoer, S., Dal Pra, S., Mazzucato, M., Frizziero, E. & Bonvin, A. M. J. J., Dec 2012, In : JOURNAL OF GRID COMPUTING. 10, 4, p. 743-767

Research output: Contribution to JournalArticleAcademicpeer-review

2010

Pushing the limits of what is achievable in protein-DNA docking: benchmarking HADDOCK's performance

van Dijk, M. & Bonvin, A. M. J. J., Sep 2010, In : Nucleic Acids Research. 38, 17, p. 5634-47 14 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Benchmarking
DNA
Proteins
Structural Models

Strengths and weaknesses of data-driven docking in critical assessment of prediction of interactions

de Vries, S. J., Melquiond, A. S. J., Kastritis, P. L., Karaca, E., Bordogna, A., van Dijk, M., Rodrigues, J. P. G. L. M. & Bonvin, A. M. J. J., 15 Nov 2010, In : Proteins. 78, 15, p. 3242-3249

Research output: Contribution to JournalArticleAcademicpeer-review

The HADDOCK web server for data-driven biomolecular docking

de Vries, S. J., van Dijk, M. & Bonvin, A. M. J. J., 2010, In : Nature Protocols. 5, 5, p. 883-897

Research output: Contribution to JournalArticleAcademicpeer-review

2009

3D-DART: a DNA structure modelling server

van Dijk, M. & Bonvin, A. M. J. J., 1 Jul 2009, In : Nucleic Acids Research. 37, p. W235-W239

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
2008

A protein-DNA docking benchmark

van Dijk, M. & Bonvin, A. M. J. J., Aug 2008, In : Nucleic Acids Research. 36, 14

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
2007

HADDOCK versus HADDOCK: New features and performance of HADDOCK2.0 on the CAPRI targets

de Vries, S. J., van Dijk, A-J., Krzeminski, M., van Dijk, M., Thureau, A., Hsu, V., Wassenaar, T. & Bonvin, A. M. J. J., Dec 2007, In : Proteins. 69, 4, p. 726-733

Research output: Contribution to JournalArticleAcademicpeer-review

2006

Information-driven protein-DNA docking using HADDOCK: it is a matter of flexibility

van Dijk, M., van Dijk, A. D. J., Hsu, V., Boelens, R. & Bonvin, A. M. J. J., 2006, In : Nucleic Acids Research. 34, 11, p. 3317-3325

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access