prof. dr. A.M.J.J. (Alexandre) Bonvin
Gegenereerd op 2015-01-28 10:11:27

Computationele structuurbiologie
Benoemingsdatum 01-09-2009

NWO-CW VICI Laureate 2006

Major research interests/expertise:

  • Biomolecular interactions
  • Biomolecular docking
  • Structure and dynamics
  • Biomolecular modelling
  • NMR spectroscopy
  • Computational structural biology





Gegenereerd op 2015-01-28 10:11:27
Curriculum vitae Download PDF

Alexandre Bonvin (1964) studied Chemistry at Lausanne University, Switzerland and obtained his PhD at Utrecht University in the Netherlands (1993). After two post-doc periods at Yale University (USA) and the ETHZ (CH) he joined Utrecht University in 1998 where he was appointed full professor of computational structural biology in 2009. In 2006, he received a prestigious VICI grant from the Dutch Research Council. He was director of chemical education from February 2009 until February 2012 and vice head of the Chemistry Department from 2010 until April 2012. He is participating to several EU projects including the FP7 WeNMR e-Infrastructure project, which he is coordinating ( His work has resulted in over 150 peer-reviewed publications (Research ID A-5420-2009).

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Research ID: A-5420-2009

ORCID ID: 0000-0001-7369-1322

Google Scholar Citations

Publications List





















  • R. Kaptein, A.M.J.J. Bonvin and R. Boelens Biomolecular structure and dynamics: recent experimental and theoretical advances. In: Proceedings of the Nato Summer School. Eds G. Vergoten and T. Theophanides Kluwer Academic Publisher, 189-209 (1997).





  • A.M.J.J. Bonvin Determination of biomolecular structures by NMR. Use of relaxation matrix calculations. PhD Thesis, Utrecht University (1993) ISBN 90-393-0408-4.

  • R.M.A. Knegtel, M. Katahira, J.G. Schilthuis, A.M.J.J. Bonvin, R. Boelens, D. Eib, CHECKCCIP.T. der Saag and R. Kaptein NMR studies of the human retinoic acid receptor-b DNA-binding domain: metal coordination and three dimensional structure. In: “Zinc-finger proteins in oncogenesis. DNA-binding and gene regulation”. M. Sluyser, G. AB, A.O. Brinkmann and R.A. Blankenstein (eds),  Annals of the New York Academy of Sciences 684, New York, 49-62 (1993).

  • A.M.J.J. Bonvin, R. Boelens and R. Kaptein Determination of biomolecular structures by NMR. Use of relaxation matrix calculations. In:”computer simulations of biomolecular systems: theoretical and experimental applications”. Vol.2. W.F. van Gunsteren, P.K. Weiner and A.J. Wilkinson (eds), ESCOM Science Publishers, 407-440 (1993).

  • A.M.J.J. Bonvin, J.A.C. Rullmann, R.M.J.N. Lamerichs, R. Boelens and R. KapteinEnsemble Iterative Relaxation Matrix Approach: a new NMR refinement protocol applied to the solution structure of crambin. PROTEINS: Structure, Function & Genetics 15, 385-400 (1993).

  • R.M.A. Knegtel, M. Katahira, J.G. Schilthuis, A.M.J.J. Bonvin, R. Boelens, D. Eib, P.T. der Saag and R. Kaptein The solution structure of the human retinoic acid receptor-b DNA-binding domain. J. Biomol. NMR 3, 1-17 (1993).


  • J.A.C. Rullmann, A.M.J.J. Bonvin, R. Boelens and R. Kaptein Structure determination from NMR - Application to crambin In: Computation of biomolecular structures: achievements, problems and perspectives.” (Proceeding of a workshop held at Schloss Ringberg, March 1990), T.M. Jovin and D.M. Soumpasis (eds.), Springer, 1-14 (1992).



Alle publicaties
  2014 - Wetenschappelijke publicaties
Ferguson, Fleur M., Dias, David M., Rodrigues, Joao P. G. L. M., Wienk, Hans, Boelens, Rolf, Bonvin, Alexandre M. J. J., Abell, Chris & Ciulli, Alessio (28-10-2014). Binding Hotspots of BAZ2B Bromodomain - Histone Interaction Revealed by Solution NMR Driven Docking. Biochemistry, 53 (42), (pp. 6706-6716) (11 p.).
Lensink, Marc F., Moal, Iain H., Bates, Paul A., Kastritis, Panagiotis L., Melquiond, Adrien S. J., Karaca, Ezgi, Schmitz, Christophe, van Dijk, Marc, Bonvin, Alexandre M. J. J., Eisenstein, Miriam, Jimenez-Garcia, Brian, Grosdidier, Solene, Solernou, Albert, Perez-Cano, Laura, Pallara, Chiara, Fernandez-Recio, Juan, Xu, Jianqing, Muthu, Pravin, Kilambi, Krishna Praneeth, Gray, Jeffrey J., Grudinin, Sergei, Derevyanko, Georgy, Mitchell, Julie C., Wieting, John, Kanamori, Eiji, Tsuchiya, Yuko, Murakami, Yoichi, Sarmiento, Joy, Standley, Daron M., Shirota, Matsuyuki, Kinoshita, Kengo, Nakamura, Haruki, Chavent, Matthieu, Ritchie, David W., Park, Hahnbeom, Ko, Junsu, Lee, Hasup, Seok, Chaok, Shen, Yang, Kozakov, Dima, Vajda, Sandor, Kundrotas, Petras J., Vakser, Ilya A., Pierce, Brian G., Hwang, Howook, Vreven, Thom, Weng, Zhiping, Buch, Idit, Farkash, Efrat, Wolfson, Haim J., Zacharias, Martin, Qin, Sanbo, Zhou, Huan-Xiang, Huang, Shen-You, Zou, Xiaoqin, Wojdyla, Justyna A., Kleanthous, Colin & Wodak, Shoshana J. (2014). Blind prediction of interfacial water positions in CAPRI. Proteins: Structure function and bioinformatics, 82 (4), (pp. 620-632) (13 p.).
Kastritis, Panagiotis L., Rodrigues, João P G L M & Bonvin, Alexandre M J J (24-03-2014). HADDOCK<sub>2P2I</sub> - A biophysical model for predicting the binding affinity of protein-protein interaction inhibitors. Journal of Chemical Information and Modeling, 54 (3), (pp. 826-836) (11 p.).
Van Ingen, Hugo & Bonvin, Alexandre M J J (01-01-2014). Information-driven modeling of large macromolecular assemblies using NMR data. Journal of Magnetic Resonance, 241 (1), (pp. 103-114) (12 p.).
Snijder, Joost, Burnley, Rebecca J, Wiegard, Anika, Melquiond, Adrien S J, Bonvin, Alexandre M J J, Axmann, Ilka M & Heck, Albert J R (28-01-2014). Insight into cyanobacterial circadian timing from structural details of the KaiB-KaiC interaction. Proceedings of the National Academy of Sciences of the United States of America, 111 (4), (pp. 1379-84) (6 p.).
Rodrigues, João P G L M & Bonvin, Alexandre M J J (01-01-2014). Integrative computational modeling of protein interactions. The FEBS journal, 281 (8), (pp. 1988-2003) (16 p.).
Rey, Martial, Sarpe, Vladimir, Burns, Kyle M., Buse, Joshua, Baker, Charles A. H., van Dijk, Marc, Wordeman, Linda, Bonvin, Alexandre M. J. J. & Schriemer, David C. (07-10-2014). Mass Spec Studio for Integrative Structural Biology. Structure, 22 (10), (pp. 1538-1548) (11 p.).
van Zundert, Gydo C P & Bonvin, Alexandre M J J (01-01-2014). Modeling protein-protein complexes using the HADDOCK webserver "modeling protein complexes with HADDOCK". Protein Structure Prediction (pp. 163-179) (17 p.).
Kastritis, Panagiotis L., Rodrigues, João P G L M, Folkers, Gert E., Boelens, Rolf & Bonvin, Alexandre M J J (15-07-2014). Proteins feel more than they see - Fine-tuning of binding affinity by properties of the non-interacting surface. Journal of Molecular Biology, 426 (14), (pp. 2632-2652) (21 p.).
Hopf, Thomas A., Schaefe, Charlotta P. I., Rodrigues, Joao P. G. L. M., Green, Anna G., Kohlbacher, Oliver, Sander, Chris, Bonvin, Alexandre M. J. J. & Marks, Debora S. (25-09-2014). Sequence co-evolution gives 3D contacts and structures of protein complexes. eLife, 3 (32 p.).
  2014 - Vakpublicaties
Vranken, W.F., Vuister, G.W. & Bonvin, Alexandre (2014). NMR-based modelling and refinement of protein 3D structures. In Andreas Kukol (Eds.), Molecular Modeling of Proteins (pp. 351-380) (32 p.). Humana Press.
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Gegenereerd op 2015-01-28 10:11:27

Research within the computational structural biology group focuses on the development of reliable bioinformatics and computational approaches to predict, model and dissect biomolecular interactions at atomic level. For this, bioinformatics data, structural information and available biochemical or biophysical experimental data are combined to drive the modelling process. This is implemented and further developed in the widely used HADDOCK software for the modelling of biomolecular complexes (

By following a holistic approach integrating various experimental information sources with computational structural biology methods we aim at obtaining a comprehensive description of the structural and dynamic landscape of complex biomolecular machines, adding the structural dimension to interaction networks and opening the route to systematic and genome-wide studies of biomolecular interactions.

Selected publications (from over 150)

  1. C. Dominguez, R. Boelens and A.M.J.J. Bonvin (2003). HADDOCK: A protein-protein docking approach based on biochemical or biophysical information. J. Am. Chem. Soc. 125, 1731-1737.
  2. A.M.J.J. Bonvin (2006). Flexible protein-protein docking. Curr. Opin. Struct. Biol., 16, 194-200.
  3. I. Gelis, A.M.J.J. Bonvin, D. Keramisanou, A. Economou and C.G. Kalodimos. Signal sequence recognition by the translocase motor SecA studied by NMR (2007). Cell, 131, 756-769.
  4. S.J. de Vries, M. van Dijk and A.M.J.J. Bonvin (2010). The HADDOCK web server for data-driven biomolecular docking. Nature Protocols, 5, 883-897.
  5. T. Schneider, Th. Kruse, R. Wimmer, I. Wiedemann, V. Sass, U. Pag, A. Jansen, A.K. Nielsen, P.H. Mygind, D.S. Raventós, S. Neve, B. Ravn, A.M.J.J. Bonvin, L. De Maria, L. Kamenova, H.-G. Sahl and H.-H. Kristensen (2010). Plectasin, a fungal defensin antibiotic peptide, targets the bacterial cell wall precursor Lipid II. Science, 328, 1168-1172.
01-06-2013 tot 30-06-2021
Algemene projectbeschrijving

The project uNMR-NL was awarded 18,5 million euro from NWO to be established as a large-scale research facility for ultra-high field NMR spectroscopy (1.2 GHz). In the new uNMR-NL facility, researchers will use magnetic nuclear resonance (NMR) and MR Imaging (MRI) to study the origin of diseases like Alzheimer’s and Parkinson’s, to identify new potential drugs, to develop new materials for batteries and solar cells and to enhance the production of crops and food quality. The project is coordinated by prof. Marc Baldus of Utrecht University and also involves the Radboud University NIjmegen, Leiden University, Wageningen University,  Eindhoven University of Technology and the public-private partnership for the analytical sciences, COAST.

Rol: Uitvoerder Financiering 2e geldstroom - NWO Projectleden
Overige projectleden:
prof. dr. Arno Kentgens (RU)
prof. dr. Marcellus Ubbink (LU)
prof. dr. Huub de Groot (LU)
prof. dr. John van Duynhoven (WUR)
prof. dr. Aldrik Velders (WUR)
dr. Henk van As (WUR)
Klaas Nicolay (TU/e)
Oscar van den Brink (COAST)

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  • Former Director of Education for the Chemistry Department (Feb. 2009- Feb. 2012)
  • Editorial board member of the Biophysical Journal  (Jun. 2008 - Jun. 2014
  • Editorial board member of Proteins
  • External advisory board member of EGI-Inspire (
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Volledige naam
prof. dr. A.M.J.J. Bonvin Contactgegevens
Hugo R. Kruytgebouw

Padualaan 8
Kamer 1.22

Telefoonnummer direct 030 253 3859
Telefoonnummer afdeling 030 253 2652
Nicolaas Bloembergengebouw

Padualaan 12
Kamer 1.22

Telefoonnummer direct 030 253 3859
Telefoonnummer afdeling 030 253 2652
Fax 030 253 7623
Gegenereerd op 2015-01-28 10:11:27
Laatst bijgewerkt op 09-01-2015