prof. dr. A.M.J.J. (Alexandre) Bonvin
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Computational Structural Biology
Date of appointment 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





Involved in the following study programme(s)
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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, has coordinated the WeNMR e-Infrastructure project ( and is leading the MoBrain Competence Center under EGI-Engage. His work has resulted in over 200 peer-reviewed publications.

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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).



All publications
  2006 - Scholarly publications
Tomaselli, Simona, Esposito, Veronica, Vangone, Paolo, Van Nuland, Nico A. J., Bonvin, Alexandre M. J. J., Guerrini, Remo, Tancredi, Teodorico, Temussi, Piero A. & Picone, Delia (01.02.2006). The α-to-β conformational transition of Alzheimer's Aβ-(1-42) peptide in aqueous media is reversible: A step by step conformational analysis suggests the location of β conformation seeding. ChemBioChem, 7 (2), (pp. 257-267) (11 p.).
  2005 - Scholarly publications
Lin, Ku-Feng, Liu, Yu-Nan, Hsu, Shang-Te D., Samuel, Dharmaraj, Cheng, Chao-Sheng, Bonvin, Alexandre M. J. J. & Lyu, Ping-Chiang (19.04.2005). Characterization and structural analyses of nonspecific lipid transfer protein 1 from mung bean. Biochemistry, 44 (15), (pp. 5703-5712) (10 p.).
van Dijk, A.D.J., De Vries, S.J., Dominguez, C., Chen, H., Zhou, H.-X. & Bonvin, A.M.J.J. (01.08.2005). Data-driven docking: HADDOCK'S adventures in CAPRI. Proteins: Structure, Function and Genetics, 60 (2), (pp. 232-238) (7 p.).
Hsu, S., Peter, C., Vangunsteren, W. & Bonvin, A. (01.01.2005). Entropy Calculation of HIV-1 Env gp120, its Receptor CD4, and their Complex: An Analysis of Configurational Entropy Changes upon Complexation. Biophysical Journal, 88 (1), (pp. 15-24).
  2004 - Scholarly publications
Tzakos, Andreas G., Fuchs, Patrick, Van Nuland, Nico A. J., Troganis, Anastasios, Tselios, Theodore, Deraos, Spyros, Matsoukas, John, Gerothanassis, Ioannis P. & Bonvin, Alexandre M. J. J. (01.08.2004). NMR and molecular dynamics studies of an autoimmune myelin basic protein peptide and its antagonist: Structural implications for the MHC II (I-A u)-peptide complex from docking calculations. Biochemistry International, 271 (16), (pp. 3399-3413) (15 p.).
Hsu, Shang-Te D., Breukink, Eefjan, Tischenko, Eugene, Lutters, Mandy A. G., De Kruijff, Ben, Kaptein, R, Bonvin, Alexandre M. J. J. & Van Nuland, Nico A. J. (01.10.2004). The nisin-lipid II complex reveals a pyrophosphate cage that provides a blueprint for novel antibiotics. Nature Structural and Molecular Biology, 11 (10), (pp. 963-967) (5 p.).
  2003 - Scholarly publications
Hsu, Shang-Te D., Breukink, Eefjan, Bierbaum, Gabriele, Sahl, Hans-Georg, De Kruijff, Ben, Kaptein, R, Van Nuland, Nico A. J. & Bonvin, Alexandre M. J. J. (11.04.2003). NMR study of mersacidin and lipid II interaction in dodecylphosphocholine micelles: Conformational changes are a key to antimicrobial activity. Journal of Biological Chemistry, 278 (15), (pp. 13110-13117) (8 p.).
  2002 - Scholarly publications
Singh, S., Folkers, G.E., Bonvin, A.M.J.J., Boelens, R., Wechselberger, R., Niztayev, A. & Kaptein, R. (15.11.2002). Solution structure and DNA-binding properties of the C-terminal domain of UvrC from E. coli. EMBO Journal, 21 (22), (pp. 6257-6266) (10 p.).
  2000 - Scholarly publications
Bonvin, A.M.J.J. (01.05.2000). Localisation and dynamics of sodium counterions around DNA in solution from molecular dynamics simulation. European Biophysics Journal, 29 (1), (pp. 57-60) (4 p.).
Bonvin, Alexandre M.J.J. & Van Gunsteren, Wilfred F. (11.02.2000). β-Hairpin stability and folding: Molecular dynamics studies of the first β-hairpin of tendamistat. Journal of Molecular Biology, 296 (1), (pp. 255-268) (14 p.).
  1998 - Scholarly publications
Sunnerhagen, Maria, Denisov, Vladimir P., Venu, Kandadai, Bonvin, Alexandre M.J.J., Carey, Jannette, Halle, Bertil & Otting, Gottfried (02.10.1998). Water molecules in DNA recognition I: Hydration lifetimes of trp operator DNA in solution measured by NMR spectroscopy. Journal of Molecular Biology, 282 (4), (pp. 847-858) (12 p.).
Bonvin, Alexandre M.J.J., Sunnerhagen, Maria, Otting, Gottfried & Van Gunsteren, Wilfred F. (02.10.1998). Water molecules in DNA recognition II: A molecular dynamics view of the structure and hydration of the trp operator. Journal of Molecular Biology, 282 (4), (pp. 859-873) (15 p.).
  1996 - Scholarly publications
Bonvin, A. M. J. J., Boelens, R. & Kaptein, R. (1996). Direct structure refinement using 3D NOE-NOE spectra of biomolecules. Journal of Magnetic Resonance (1969), 95 (3), (pp. 626-631).
Bonvin, Alexandre & Brünger, A.T. (01.01.1996). Do NOE distances contain enough information to assess the relative populations of multi-conformer structures?. Journal of Biomolecular NMR, 7 (1), (pp. 72-76) (5 p.).
  1995 - Scholarly publications
SLIJPER, M, Bonvin, Alexandre, BOELENS, R & KAPTEIN, R (1995). Application of structure refinement using 3D NOE-NOE spectroscopy to Lac Repressor Headpiece (1-56). Journal of Magnetic Resonance - Series B, 107 (3), (pp. 298-301).
  1994 - Scholarly publications
Bonvin, A.M.J.J., Boelens, R. & Kaptein, R. (01.05.1994). Direct nuclear overhauser effect refinement of crambin from two- dimensional NMR data using a slow-cooling annealing protocol. Biopolymers, 34 (1), (pp. 39-50) (12 p.).
  1993 - Scholarly publications
Bonvin, A.M.J.J., Rullmann, J.A.C., Lamerichs, R.M.J.N., Boelens, R. & Kaptein, R. (01.05.1993). 'Ensemble' iterative relaxation matrix approach: A new NMR refinement protocol applied to the solution structure of crambin. Proteins: Structure, Function and Genetics, 15 (4), (pp. 385-400) (16 p.).
  1991 - Scholarly publications
Bonvin, A.M., Boelens, R. & Kaptein, R. (01.09.1991). Direct NOE refinement of biomolecular structures using 2D NMR data. Journal of Biomolecular NMR, 1 (3), (pp. 305-309) (5 p.).
Gonzalez, C., Rullmann, J. A. C., Bonvin, A. M. J. J., Boelens, R. & Kaptein, R. (1991). Toward an NMR R factor. Journal of Magnetic Resonance (1969), 91 (3), (pp. 659-664).
  1990 - Scholarly publications
Burghardt, Irene, Di Bari, Lorenzo, Bonvin, Alexandre & Bodenhausen, Geoffrey (1990). Effects of strong coupling in multiple-quantum-filtered two-dimensional NOE spectroscopy. Journal of Magnetic Resonance (1969), 86 (3), (pp. 652-656).
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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.
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Additional functions and activities
  • 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: Structure, Function & Bioinformatics (since 2006)
  • Editorial Board and Editorial manager for Protein Engineering, Design, and Selection (since 2014)
  • External advisory board member of EGI-Inspire ( (2010-2015)
  • Member of the CAPRI (Critical Assessment of Predicted Interaction) committee (since 2013)
  • Member of the wwPDB task force on integrative models (2014-2015)
  • Member of the programme advisory committee of SURFSara for compute and data infrastructures (since 2016)
  • Scientific advisory board member of the EMBL-EBI Molecular and Cellular Structure cluster (former PDBe)  (since Oct. 2016)
  • Advisory council member of the Institute of Biomedical Sciences (IBMS), Academia Sinica, Taiwan, Jan. 2017-present
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Full name
prof. dr. A.M.J.J. Bonvin Contact details

Nicolaas Bloembergen building

Padualaan 8

3584CH Utrecht


Room 1.22

Phone: +31 30 2533859

Phone (secr.): +31 30 2532652

Accessible via Kruyt Building -> first floor -> bridge to Sjoerd Groenman Building

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Last updated 13.06.2018