prof. dr. A.M.J.J. (Alexandre) Bonvin
Gegenereerd op 2016-05-30 20:18:12

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





Wetenschappelijke expertises
Gegenereerd op 2016-05-30 20:18:12
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 has been coordinating ( His work has resulted in over 180 peer-reviewed publications (Research ID  A-5420-2009; ORCID 0000-0001-7369-1322).

Gegenereerd op 2016-05-30 20:18:12

Research ID: A-5420-2009

ORCID ID: 0000-0001-7369-1322

Google Scholar Citations

Publications List



  • M.F. Lensink, S. Velankar, A. Kryshtafovych, S. Huang, D. Schneidman-Duhovny, A. Sali, J. Segura, N.s Fernandez-Fuentes, S. Viswanath, R. Elber, S. Grudinin, P. Popov, E. Neveu, Hasup Lee, M. Baek, S. Park, L. Heo, G. Rie Lee, C. Seok, S. Qin, H. Zhou, D.W. Ritchie, B. Maigret, M. Devignes, A. Ghoorah, M. Torchala, R.A.G. Chaleil, P.A. Bates, E.t Ben-Zeev, M. Eisenstein, S.S. Negi, Z. Weng, T. Vreven, B.G. Pierce, T. M. Borrman, J. Yu, F. Ochsenbein, R. Guerois, A. Vangone, J.P.G.L.M. Rodrigues, G. van Zundert, M. Nellen, L. Xue, E. Karaca, A.S.J. Melquiond, K. Visscher, P.L. Kastritis, A.M.J.J. Bonvin, X. Xu, L. Qiu, C. Yan, J. Li, Z. Ma, J. Cheng, X. Zou, Y. Shen, L.X. Peterson, H. Kim, A. Roy, X. Han, J. Esquivel-Rodriguez, D. Kihara, X. Yu, N.J. Bruce, J.C. Fuller, R.C. Wade, I. Anishchenko, P.J. Kundrotas, I.A. Vakser, K. Imai, K.i Yamada, T. Oda, T. Nakamura, K. Tomii, C. Pallara, M. Romero-Durana, B. Jimenez-Garcia, I.H. Moal, J Fernandez-Recio, J. Young Joung, J. Yun Kim, K.g Joo, J. Lee, D. Kozakov, S. Vajda, S. Mottarella, D.R. Hall, D. Beglov, A. Mamonov, B. Xia, T. Bohnuud, C.A. Del Carpio, E. Ichiishi, N. Marze, D. Kuroda, S.S. Roy Burman, J.J. Gray, E. Chermak, L. Cavallo, R. Oliva, A. Tovchigrechko and S.J. Wodak. Prediction of homo- and hetero-protein complexes by ab-initio and template-based docking: a CASP-CAPRI experiment Proteins: Struc. Funct. & Bioinformatics, In press (2016)

  • P. Sliz, P. Meyer, S. Socias, J. Key, E. Ransey, E.C. Tjon, A. Buschiazzo, M. Lei, C. Botka, J. Withrow, D.B. Neau, K. Rajashankar, K.S. Anderson, R. Baxter, S. Blacklow, T. Boggon, A.M.J.J. Bonvin, D. Borek, T. Brett, A. Caflisch, C. Chang, W. Chazin, K.D. Corbett, M. Cosgrove, S. Crosson, S. Dhe-Paganon, E. Di Cera, C. Drennan, M. Eck, B. Eichman, Q. Fan, A. Ferré-D’Amaré, J.S. Fraser, J.C. Fromme, K. Garcia, R. Gaudet, P. Gong, S. Harrison, E. Heldwein, Z. Jia, R. Keenan, A. Kruse, M. Kvansakul, J. McLellan, Y. Modis, Y. Nam, Zb. Otwinowski, E.F. Pai, P.J. Barbosa Pereira, C. Petosa, C.S. Raman, T. Rapoport, A. Roll-Mecak, M. Rosen, G. Rudenko, J. Schlessinger, T. Schwartz, Y. Shamoo, H. Sondermann, Y. Tao, N. Tolia, O.V. Tsodikov, K.D. Westover, H. Wu, I. Foster, F. Maia, T. Gonen, T. Kirchhausen, K. Diederichs and M. Crosas. Data publication with the structural biology data grid supports live analysis. Nature Communications, In Press (2016).

  • S. Jung, J. Fischer, B. Spudy, K. Tim, F.D. Soennichsen, L. Xue, A.M.J.J. Bonvin, P. Goettig, V. Magdolen, U. Meyer-Hoffert, J. Grötzinger. The solution structure of the kallikrein-related peptidases inhibitor SPINK6Biochemical and Biophysical Research Communications, Advanced Online Publication (2016).

  • E. Deplazes, J. Davies, A.M.J.J. Bonvin, G.F. King and A.E. Mark. On the Combination of Ambiguous and Unambiguous Data in the Restraint-driven Docking of Flexible Peptides with HADDOCK: The Binding of the Spider Toxin PcTx1 to the Acid Sensing Ion channel (ASIC)1aJ. Chem. Inf. and Model., Advanced Online Publication (2016).

  • J.P.G.L.M. Rodrigues, A.S.J. Melquiond and  A.M.J.J. BonvinMolecular Dynamics Characterization of the Conformational Landscape of Small Peptides: A series of hands-on collaborative practical sessions for undergraduate studentsBiochemistry and Molecular Biology Education, Advanced Online Publication (2016).

  • A. Vangone, R. Oliva, L. Cavallo and A.M.J.J. Bonvin. Prediction of Biomolecular Complexes. In: From Protein Structure to Function with Bioinformatics. Ed. Daniel John Rigden, Springer, In Press.

  • R. Zhang, T. Eckert, T. Lutteke, S. Hanstein, A. Scheidig, A.M.J.J. Bonvin, N.E. Nifantiev, T. Kozar, R. Schauer, M. Abdulaziz Enani and H.C. Siebert. Structure-function relationship of antimicrobial peptides and proteins in respect to contact-molecules on pathogen surfacesCurrent Topics in Medicinal Chemistry16, 89-98 (2016).





















  • 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
  2016 - Wetenschappelijke publicaties
Garcia Lopes Maia Rodrigues, João, Melquiond, Adrien S J & Bonvin, Alexandre M J J (11-01-2016). Molecular dynamics characterization of the conformational landscape of small peptides - A series of hands-on collaborative practical sessions for undergraduate students. Biochemistry and molecular biology education © 2016 The International Union of Biochemistry and Molecular Biology..
Zhang, Ruiyan, Eckert, Thomas, Lutteke, Thomas, Hanstein, Stefan, Scheidig, Axel, Bonvin, Alexandre M J J, Nifantiev, Nikolay E, Kozar, Tibor, Schauer, Roland, Enani, Mushira Abdulaziz & Siebert, Hans-Christian (2016). Structure-Function Relationships of Antimicrobial Peptides and Proteins with Respect to Contact Molecules on Pathogen Surfaces. Current Topics in Medicinal Chemistry, 16 (1), (pp. 89-98) (10 p.).
Jung, Sascha, Fischer, Jan, Spudy, Björn, Kerkow, Tim, Sönnichsen, Frank D, Xue, Li, Bonvin, Alexandre M J J, Goettig, Peter, Magdolen, Viktor, Meyer-Hoffert, Ulf & Grötzinger, Joachim (29-01-2016). The solution structure of the kallikrein-related peptidases inhibitor SPINK6. Biochemical and Biophysical Research Communications Copyright © 2016. Published by Elsevier Inc..
  2015 - Wetenschappelijke publicaties
C.p.van Zundert, Gydo & M.j.j. Bonvin, Alexandre (01-01-2015). Fast and sensitive rigid-body fitting into cryo-EM density maps with PowerFit. AIMS Biophysics, 2 (2), (pp. 73-87) (15 p.).
Kalia, Munishikha, Willkomm, Sarah, Claussen, Jens Christian, Restle, Tobias & Bonvin, Alexandre M J J (2015). Novel Insights into Guide RNA 5'-Nucleoside/Tide Binding by Human Argonaute 2. International Journal of Molecular Sciences, 17 (1).
van Zundert, G C P, Garcia Lopes Maia Rodrigues, João, Trellet, M, Schmitz, C, Kastritis, P L, Karaca, E, Melquiond, A S J, van Dijk, Marc, de Vries, S J & Bonvin, A M J J (26-09-2015). The HADDOCK2.2 Web Server - User-Friendly Integrative Modeling of Biomolecular Complexes. Journal of Molecular Biology Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved..
  2011 - Wetenschappelijke publicaties
Kastritis, Panagiotis L. & Bonvin, Alexandre M. J. J. (04-02-2011). Erratum: Are scoring functions in protein - Protein Docking Ready to predict interactomes? Clues from a novel binding affinity benchmark (Journal of Proteome Research (2010) 9 (2216-2225). Journal of Proteome Research, 10 (2), (pp. 921-922) (2 p.).
Koehler, Christian, Carlier, L.P.A., Veggi, Daniele, Balducci, Enrico, Di Marcello, Federica, Ferrer-Navarro, Mario, Pizza, Mariagrazia, Daura, Xavier, Soriani, Marco, Boelens, Rolf & Bonvin, Alexandre M. J. J. (29-04-2011). Structural and biochemical characterization of NarE, an iron-containing ADP-ribosyltransferase from Neisseria meningitidis. Journal of Biological Chemistry, 286 (17), (pp. 14842-14851) (10 p.).
  2009 - Wetenschappelijke publicaties
Eggink, Dirk, Langedijk, Johannes P.M., Bonvin, Alexandre M.J.J., Deng, Yiqun, Lu, Min, Berkhout, Ben & Sanders, Rogier W. (25-09-2009). Detailed mechanistic insights into HIV-1 sensitivity to three generations of fusion inhibitors. Journal of Biological Chemistry, 284 (39), (pp. 26941-26950) (10 p.).
Van Wijk, Sjoerd J. L., De Vries, Sjoerd J., Kemmeren, Patrick, Huang, Anding, Boelens, Rolf, Bonvin, Alexandre M. J. J. & Timmers, H Th Marc (20-01-2009). Erratum: A comprehensive framework of E2-RING E3 interactions of the human ubiquitin-proteasome system (Molecular Systems Biology (2009) 5 (295) DOI: 10.1038/msb.2009.55). Molecular Systems Biology [E], 5.
  2007 - Wetenschappelijke publicaties
De Vries, Sjoerd J., Van Dijk, Aalt D. J., Krzeminski, Mickaël, van Dijk, Marc, Thureau, A.J.M.M., Hsu, Victor, Wassenaar, T.A. & Bonvin, Alexandre M. J. J. (01-12-2007). HADDOCK versus HADDOCK: New features and performance of HADDOCK2.0 on the CAPRI targets. Proteins: Structure function and bioinformatics, 69 (4), (pp. 726-733) (8 p.).
Van Dijk, Aalt D. J., Ciofi-Baffoni, Simone, Banci, Lucia, Bertini, Ivano, Boelens, Rolf & Bonvin, Alexandre M. J. J. (01-04-2007). Modeling protein-protein complexes involved in the cytochrome c oxidase copper-delivery pathway. Journal of Proteome Research, 6 (4), (pp. 1530-1539) (10 p.).
Tomaselli, Simona, Ragona, Laura, Zetta, Lucia, Assfalg, Michael, Ferranti, Pasquale, Longhi, Renato, Bonvin, Alexandre M.J.J. & Molinari, Henriette (01-10-2007). NMR-based modeling and binding studies of a ternary complex between chicken liver bile acid binding protein and bile acids. Proteins: Structure function and bioinformatics, 69 (1), (pp. 177-191) (15 p.).
Gelis, Ioannis, Bonvin, Alexandre M.J.J., Keramisanou, Dimitra, Koukaki, Marina, Gouridis, Giorgos, Karamanou, Spyridoula, Economou, Anastassios & Kalodimos, Charalampos G. (16-11-2007). Structural Basis for Signal-Sequence Recognition by the Translocase Motor SecA as Determined by NMR. Cell, 131 (4), (pp. 756-769) (14 p.).
  2006 - Wetenschappelijke publicaties
Volkov, Alexander N., Ferrari, Davide, Worrall, Jonathan A.R., Bonvin, Alexandre M.J.J. & Ubbink, Marcellus (16-06-2006). Erratum: The orientations of cytochrome c in the highly dynamic complex with cytochrome b5visualized by NMR and docking using HADDOCK (Protein Science (2005) 14 (799-811)). Protein Science, 15 (6), (pp. 1563) (1 p.).
  2005 - Wetenschappelijke publicaties
Salinas, Roberto Kopke, Folkers, Gert E., Bonvin, Alexandre M. J. J., Das, Devashish, Boelens, Rolf & Kaptein, R (01-09-2005). Altered specificity in DNA binding by the lac repressor: A mutant lac headpiece that mimics the gal repressor. ChemBioChem, 6 (9), (pp. 1628-1637) (10 p.).
  2003 - Wetenschappelijke publicaties
Hsu, S.T., Breukink, E.J., Bierbaum, G., Sahl, H.-G., de Kruijff, B., Kaptein, R., van Nuland, N.A.J. & Bonvin, A.M.J.J. (2003). NMR study of mersacidin and lipid II interaction in dodecylphosphocholine micelles. Journal of Biological Chemistry, 278, (pp. 13110-13117) (8 p.).
  2002 - Wetenschappelijke publicaties
Hsu, S., Breukink, E.J., de Kruijff, B., Kaptein, R., Bonvin, A.M.J.J. & van Nuland, N.A.J. (2002). Mapping the targeted membrane pore formation mechanism by solution NMR: the nisin Z and lipid II interaction in SDS micelles. Biochemistry, 41, (pp. 7670-7676) (7 p.).
  1993 - Wetenschappelijke publicaties
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Gegenereerd op 2016-05-30 20:18:12

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 2016-05-30 20:18:12
  • 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 wwPDB task force on integrative models (2014-2015)
Gegenereerd op 2016-05-30 20:18:12
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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 2016-05-30 20:18:12
Laatst bijgewerkt op 23-05-2016