prof. dr. A.M.J.J. (Alexandre) Bonvin
Gegenereerd op 2017-07-27 16:54:05

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 2017-07-27 16:54:05
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 190 peer-reviewed publications.

Gegenereerd op 2017-07-27 16:54:05

Research ID: A-5420-2009

ORCID ID: 0000-0001-7369-1322

Google Scholar Citations

Publications List



  • C. Geng, S. Narasimhan, J. P.G.L.M. Rodrigues and A.M.J.J. Bonvin. Information-driven, ensemble flexible peptide docking using HADDOCK. Methods in Molecular Biology: Modeling Peptide-Protein Interactions. Eds Ora Schueler-Furman and Nir London. Humana Press Inc. In press (2017).

  • R.C.G. de Bruin, A.G.M. Stam, A. Vangone, P. van Bergen en Henegouwen, H.M.W. Verheul, A.M.J.J. Bonvin, T.D. de Gruijl, H.J. van der Vliet. Prevention of Vγ9Vδ2-T cell activation by a Vγ9Vδ2-TCR nanobodyJournal of Immunology198, 308-317 (2017).

  • T. Bohnuud, L. Luo, S.J. Wodak, A.M.J.J. Bonvin, Z. Weng, S. Vajda, O. Schueler-Furman and D. Kozakov. A benchmark testing ground for integrating homology modeling and protein dockingProteins: Struc. Funct. & Bioinformatics85, 10-17 (2017).





















  • 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
  2017 - Wetenschappelijke publicaties
de Bruin, Renée C G, Stam, Anita G M, Vangone, Anna, van Bergen En Henegouwen, Paul M P, Verheul, Henk M W, Sebestyén, Zsolt, Kuball, Jürgen, Bonvin, Alexandre M J J, de Gruijl, Tanja D & van der Vliet, Hans J (01-05-2017). Correction: Prevention of Vγ9Vδ2 T Cell Activation by a Vγ9Vδ2 TCR Nanobody. Journal of Immunology, 198 (9), (pp. 3759) (1 p.).
Geng, Cunliang, Narasimhan, Siddarth, Garcia Lopes Maia Rodrigues, João & Bonvin, Alexandre M J J (2017). Information-Driven, Ensemble Flexible Peptide Docking Using HADDOCK. In Ora Schueler-Furman & Nir London (Eds.), Modeling Peptide-Protein Interactions - Methods and Protocols (pp. 109-138) (30 p.). New York: Springer Science & Business Media, LLC.
Vangone, A, Garcia Lopes Maia Rodrigues, João, Xue, L C, van Zundert, G C P, Geng, C, Kurkcuoglu Soner, Zeynep, 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 (2017). Sense and simplicity in HADDOCK scoring - Lessons from CASP-CAPRI round 1. Proteins: Structure, Function and Genetics, 85 (3), (pp. 417–423). © 2016 The Authors Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc..
van Zundert, G. C P, Trellet, M., Schaarschmidt, J., Kurkcuoglu Soner, Zeynep, David, M., Verlato, M., Rosato, A. & Bonvin, A. M J J (03-02-2017). The DisVis and PowerFit Web Servers - Explorative and Integrative Modeling of Biomolecular Complexes. Journal of Molecular Biology, 429 (3), (pp. 399-407) (9 p.).
  2016 - Wetenschappelijke publicaties
de Bruin, Renée C G, Stam, Anita G M, Vangone, Anna, van Bergen En Henegouwen, Paul M P, Verheul, Henk M W, Sebestyén, Zsolt, Kuball, Jürgen, Bonvin, Alexandre M J J, de Gruijl, Tanja D & van der Vliet, Hans J (28-11-2016). Prevention of Vγ9Vδ2 T Cell Activation by a Vγ9Vδ2 TCR Nanobody. Journal of Immunology, 198, (pp. 308-317) (10 p.). Copyright © 2016 by The American Association of Immunologists, Inc..
Xue, Li, Garcia Lopes Maia Rodrigues, João, Kastritis, Panagiotis L, Bonvin, Alexandre Mjj & Vangone, Anna (01-12-2016). PRODIGY - a web server for predicting the binding affinity of protein-protein complexes. Bioinformatics, 32 (23), (pp. 3676-3678) (3 p.). © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail:
Felix, Jan, Kandiah, Eaazhisai, De Munck, Steven, Bloch, Yehudi, Van Zundert, Gydo C P, Pauwels, Kris, Dansercoer, Ann, Novanska, Katka, Read, Randy J., Bonvin, Alexandre M J J, Vergauwen, Bjorn, Verstraete, Kenneth, Gutsche, Irina & Savvides, Savvas N. (07-11-2016). Structural basis of GM-CSF and IL-2 sequestration by the viral decoy receptor GIF. Nature Communications, 7 (13 p.).
Grinter, Rhys, Josts, Inokentijs, Mosbahi, Khedidja, Roszak, Aleksander W., Cogdell, Richard J., Bonvin, Alexandre M J J, Milner, Joel J., Kelly, Sharon M., Byron, Olwyn, Smith, Brian O. & Walker, Daniel (31-10-2016). Structure of the bacterial plant-ferredoxin receptor FusA. Nature Communications, 7.
  2006 - Wetenschappelijke publicaties
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 - Wetenschappelijke publicaties
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 - Wetenschappelijke publicaties
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 - Wetenschappelijke publicaties
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 - Wetenschappelijke publicaties
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 - Wetenschappelijke publicaties
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 - Wetenschappelijke publicaties
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 - Wetenschappelijke publicaties
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).
  1995 - Wetenschappelijke publicaties
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 - Wetenschappelijke publicaties
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 - Wetenschappelijke publicaties
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 - Wetenschappelijke publicaties
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 - Wetenschappelijke publicaties
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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Gegenereerd op 2017-07-27 16:54:06

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.
Gegenereerd op 2017-07-27 16:54:06
  • 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)
  • Lid van de Programma Advies Raad van SURFSara voor Reken- en Data-infrastructuren (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
Gegenereerd op 2017-07-27 16:54:06
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prof. dr. A.M.J.J. Bonvin Contactgegevens

Nicolaas Bloembergengebouw

Padualaan 8

3584 CH Utrecht


Kamer 1.22

Phone: +31 30 2533859

Phone (secr.): +31 30 2532652

Accessible via Kruytgebouw -> first floor -> bridge to Sjoerd Groenmangebouw

Gegenereerd op 2017-07-27 16:54:06
Laatst bijgewerkt op 13-06-2017