Alexandre Bonvin bio photo

Computational Structural Biology group focusing on dissecting, understanding and predicting biomolecular interactions at the molecular level.

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  • P.I. Koukos, L.C. Xue and A.M.J.J. Bonvin. Protein-ligand pose and affinity prediction. Lessons from D3R Grand Challenge 3. J. Comp. Aid. Mol. Des. In Press (2018).

  • D. Salomoni, I. Campos, L. Gaido, J. Marco de Lucas, P. Solagna, J. Gomes, L. Matyska, P. Fuhrman, M. Hardt, G. Donvito, L. Dutka, M. Plociennik, R. Barbera, I. Blanquer, A. Ceccanti, E. Cetinic, M. David, C. Duma, A. López-García, G. Moltó, P. Orviz, Z. Sustr, M. Viljoen, F. Aguilar, L. Alves, M. Antonacci, L. A. Antonelli, S. Bagnasco, A.M.J.J. Bonvin, R. Bruno, Y. Chen, A. Costa, D. Davidovic, B. Ertl, M. Fargetta, S. Fiore, S. Gallozzi, Z. Kurkcuoglu, L. Lloret, J. Martins, A. Nuzzo, P. Nassisi, C. Palazzo, J. Pina, E. Sciacca, D. Spiga, M. Tangaro, M. Urbaniak, S. Vallero, B. Wegh, V. Zaccolo, F. Zambelli, T. Zok. INDIGO-DataCloud: a Platform to Facilitate Seamless Access to E-Infrastructures. J. Grid. Comp. Advanced Online Publication (2018).

  • K. Elez, A.M.J.J. Bonvin* and A. Vangone*. Distinguishing crystallographic from biological interfaces in protein complexes: Role of intermolecular contacts and energetics for classification. BMC Bioinformatics, In press (2018).

  • A.M.J.J. Bonvin, E. Karaca, P.L. Kastritis & J.P.G.L.M. Rodrigues. Correspondence: Defining distance restraints in HADDOCK. Nature Protocols 13, 1503 (2018). Free online only access

  • M.J. Abraham, A.S.J. Melquiond, E. Ippoliti, V. Gapsys, B. Hess, M. Trellet, J.P.G.L.M. Rodrigues, E. Laure, R. Apostolov, B.L. de Groot, A.M.J.J. Bonvin, E. Lindahl. BioExcel Whitepaper on Scientific Software Development. Zenodo (2018).

  • A.M.J.J. Bonvin, C. Geng, M. van Dijk, E. Karaca, P. L. Kastritis, P.I. Koukos, Z. Kurkcuoglu, A.S.J. Melquiond, J.P.G.L.M. Rogridues, J. Schaarschmidt, C. Schmitz, J. Roel-Touris, M.E. Trellet, S. de Vries, A. Vangone, L. Xue, G.C.P. van Zundert HADDOCK. In Encyclopedia of Biophysics, In press (2018).

  • A.J. Preto, J.G. Almeida, J. Schaarschmidt, L.C. Xue, I.S. Moreira and A.M.J.J. Bonvin. Computational tools for the structural characterization of proteins and their complexes from sequence-evolutionary data. Encyclopedia of Analytical Chemistry In press (2018),

  • S. Narasimhan, D. Mance, C. Pinto, M. Weingarth, A.M.J.J. Bonvin and Marc Baldus. Rapid Prediction of Multi-dimensional NMR Data Sets Using FANDAS. In: Methods in Molecular Biology: Protein NMR Humana Press, New York, NY, 111-132 (2018).

  • J. Schaarschmidt, B. Monastyrskyy, A.y Kryshtafovych and A.M.J.J. Bonvin. Assessment of Contact Predictions in CASP12: Co-Evolution and Deep Learning Coming of Age. Proteins: Struc. Funct. & Bioinformatics 86(S1), 51-66 (2018).

  • Z. Kurkcuoglu, P.I. Koukos, N. Citro, M.E. Trellet, J.P.G.L.M. Rodrigues, I.S. Moreira, J. Roel-Touris, A.S.J. Melquiond, C. Geng, J. Schaarschmidt, L.C. Xue, A. Vangone and A.M.J.J. Bonvin. Performance of HADDOCK and a simple contact-based protein-ligand binding affinity predictor in the D3R Grand Challenge 2. J. Comp. Aid. Mol. Des. 32, 175-185 (2018).






















  • 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. Kaptein Ensemble 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).