Research Output 2006 2018

  • 21 Article
  • 3 PhD Thesis - Research VU, graduation VU
2017

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: Scientific - peer-reviewArticle

Open Access

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: Scientific - peer-reviewArticle

2016

Fetal and maternal genes in pregnancy-associated diseases

Thulluru, H. K. 2016

Research output: ScientificPhD Thesis - Research VU, graduation VU

Open Access
File

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: Scientific - peer-reviewArticle

Open Access
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: Scientific - peer-reviewArticle

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: Scientific - peer-reviewArticle

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: Scientific - peer-reviewArticle

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: Scientific - peer-reviewArticle

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: Scientific - peer-reviewArticle

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: Scientific - peer-reviewArticle

The role of transcription factor STOX1A in transcriptional networks associated with neurodegeneration

van Abel, D. 2012

Research output: ScientificPhD Thesis - Research VU, graduation VU

Open Access
File

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: Scientific - peer-reviewArticle

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: Scientific - peer-reviewArticle

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: Scientific - peer-reviewArticle

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: Scientific - peer-reviewArticle

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: Scientific - peer-reviewArticle

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: Scientific - peer-reviewArticle

2008

A protein-DNA docking benchmark

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

Research output: Scientific - peer-reviewArticle

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: Scientific - peer-reviewArticle

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: Scientific - peer-reviewArticle