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Computational Structural Biology Group Utrecht University

Contact Details

Utrecht University

Padualaan 8, 3584 CH Utrecht

Prof. dr. A.M.J.J. Bonvin

0031 (0)30 2533859

Hotel Description

Research within the computational structural biology group of Alexandre Bonvin at the Bijvoet Center for Biomolecular Research of the Faculty of Science of Utrecht University 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. Alexandre Bonvin is the coordinator of WeNMR an EU FP7 funded e-Infrastructure for structural biology.

Structural biology
  • Biomedical & health
  • Industrial biotech
  • Other
  • Biomolecular interactions
  • Biomolecular complexes
  • Protein-ligand interactions
  • Structure and function
  • Structure and dynamics
  • No specific area - focus is on methodological developments

Expertise and Track Record

Our facility provides a worldwide unique repository of tools and services and therefore also represents the largest life science Virtual Research Community (VRC) supported by the European Grid Infrastructure (EGI http://www.egi.eu).

Coordinator of the FP7 EU e-Infrastructure project WeNMR (www.wenmr.eu)

Serving with our HADDOCK portal a large (>4600) worldwide user community

Experience in integrative structural biology, combining NMR, MS, SAXS, cryo-EM and other biophysically-derived data, together with bioinformatics information to drive the modelling process.

See: J.P.G.L.M Rodrigues and A.M.J.J. Bonvin
“Integrative computational modeling of protein interactions.”
FEBS J., 281, 1988-2003 (2014).

  • Alex S, Lange K, Amolo T, Grinstead JS, Haakonsson AK, Szalowska E, Koppen A, Mudde K, Haenen D, Al-Lahham S, Roelofsen H, Houtman R, van der Burg B, Mandrup S, Bonvin AM, Kalkhoven E, Müller M, Hooiveld GJ, Kersten S. Short-chain fatty acids stimulate angiopoietin-like 4 synthesis in human colon adenocarcinoma cells by activating peroxisome proliferator-activated receptor γ. Mol Cell Biol. 2013 Apr;33(7):1303-16. doi: 10.1128/MCB.00858-12. Our contribution in this paper was the structural modelling and interpretation of short fatty acid modecules into the nuclear receptor peroxisome proliferator activated receptor using our HADDOCK software.
  • Fiamegos YC, Kastritis PL, Exarchou V, Han H, Bonvin AM, Vervoort J, Lewis K, Hamblin MR, Tegos GP. Antimicrobial and efflux pump inhibitory activity of caffeoylquinic acids from Artemisia absinthium against gram-positive pathogenic bacteria. PLoS One. 2011 Apr 4;6(4):e18127. doi: 10.1371/journal.pone.0018127. Our contribution in this paper was the modelling and interpretation of several protein-ligand complexes using our HADDOCK software.
  • Schneider T, Kruse T, Wimmer R, Wiedemann I, Sass V, Pag U, Jansen A, Nielsen AK, Mygind PH, Raventós DS, Neve S, Ravn B, Bonvin AM, De Maria L, Andersen AS, Gammelgaard LK, Sahl HG, Kristensen HH. Plectasin, a fungal defensin, targets the bacterial cell wall precursor Lipid II. Science. 2010 May 28;328(5982):1168-72. doi: 10.1126/science.1185723. Our contribution in this Science paper was the modelling and interpretation of the plectasin-lipidII complex based on NMR chemical shift perturbation data using our HADDOCK software.
  • J. Snijder, R.J. Burnley, A. Wiegard, A.S.J. Melquiond, A.M.J.J. Bonvin, I.M. Axmann, A.J.R. Heck. Insight into cyanobacterial circadian timing from structural details of the KaiB-KaiC interaction. Proc. Natl. Acad. Sci. USA. 111, 1379-1383 (2014).
  • D.L. Hulsik, Y.Y. Liu, N.M. Strokappe, S. Battella, M. El Khattabi, L.E. McCoy, A. Hinz, M. Hock, A.M.J.J. Bonvin, J.P.M. Langedijk, D. Davis, A. Forsman Quinley, M. Aasa-Chapman, R.A. Weiss, C.T. Verrips, W. Weissenhorn and L. Rutten "A gp41 MPER-specific Llama VHH Requires a Hydrophobic CDR3 for Neutralization but not for Antigen Recognition." PloS Pathogens, 9, e1003202 (2013)
  • R. Dagil, C O'Shea, A. Nykaer, A.M.J.J. Bonvin and B.B. Kragelund "Gentamicin Binds to Megalin as a Competitive Inhibitor and Utilizes the Common Ligand Binding Motif of Complement Type Repeats." J. Biol. Chem, 288, 4424-4435 (2013).
  • E. Escobar-Cabrera, Okon, D.K.W. Lau, C.F. Dart, A.M.J.J. Bonvin and L.P. McIntosh "Characterizing the N- and C-terminal SUMO interacting motifs of the scaffold protein DAXX." J. Biol. Chem., 286, 19816-19829 (2011).
  • K.M. Varney#, A.M.J.J. Bonvin#, M. Pazgier#, J. Malin#, W. Yu#, E. Ateh, T. Oashi, J. Huang, W. Lu, M. Diepeveen-de Buin, J. Bryant, E. Breukink, A.D. MacKerell Jr. and E.P.H. de Leeuw "Turning Defense into Offense: Development of Defensin Mimetics as Novel Antibiotics targeting Lipid II." PloS Pathogens, 9, e1003732. doi:10.1371/journal.ppat.1003732 (2013).

The tools and expertise offered is part of the EU funded e-Infrastructure WeNMR, which is coordinated by Alexander Bonvin. It brings together a diverse group of stakeholders and has also tight connections with various European Research Infrastructure projects (e.g. BioNMR) and the ESFRI Instruct project;In addition to research communities, WeNMR also reaches out to the e-Infrastructure resource providers at regional, national (NGIs) and European (EGI) levels and even worldwide (e.g. via connections to Open Science Grid and XSEDE in the US) levels and to researchers in industry.

Hotel Characteristics

  • Three Linux clusters for >1600 CPU cores and >120TB disk storage. Access to European Grid infrastructure (>90'000 CPU cores)