Alexandre Bonvin bio photo

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

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Publications

2021

  • G. Dudas, S. Hong, B. Potter, S. Calvignac-Spencer, F. Niatou-Singa, T. Tombolomako, T. Fuh-Neba, U. Vickos, M. Ulrich, F. Leendertz, K. Khan, C. Huber, A. Watts, I. Olendraitė, J. Snijder, K. Wijnant, A.M.J.J. Bonvin, P. Martres, S. Behillil, A. Ayouba, M. Maidadi, D. Djomsi, C. Godwe, C. Butel, A. Šimaitis, M. Gabrielaite, M. Katėnaitė, R. Norvilas, L. Raugaitė, G. Koyaweda, J. Kaleb Kandou, R. Jonikas, I. Nasvytienė, Ž. Žemeckienė, D. Gečys, K. Tamušauskaitė, M. Norkienė, E. Vasiliūnaitė, D. Žiogienė, A. Timinskas, M. Šukys, M. Šarauskas, G. Alzbutas, A. Amuri, E. Lusamaki, J. Makangara, F. Muyembe, E. Lofiko, P. Mbala, J. Muyembe-Tamfum, M. Darnycka Belizaire, R. Essomba, M. Claire Assoumou, A. Mboringong, A. Baba Dieng, D. Juozapaitė, S. Hosch, J. Obama, M. Ondo’o Ayekaba, D. Naumovas, A. Pautienius, C. Rafaï, A. Vitkauskienė, R. Ugenskienė, A. Gedvilaitė, D. Čereškevičius, V. Lesauskaitė, L. Žemaitis, L. Griškevičius and G. Baele. Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like mutations and deletion. Nature Comm. In press (2021). Preprint available here.

  • M.F. Lensink, G. Brysbaert, T. Mauri, N. Nadzirin, S. Velankar, R.A.G. Chaleil, T. Clarence, P.A. Bates, R. Kong, B. Liu, G. Yang, M. Liu, H. Shi, X. Lu, S. Chang, R.S. Roy, F. Quadir, J. Liu, J. Cheng, A. Antoniak, C. Czaplewski, A. Giełdoń, M. Kogut, A.G. Lipska, A. Liwo, E.A. Lubecka, M. Maszota-Zieleniak, A.K. Sieradzan, R. Ślusarz, P.A. Wesołowski, K. Zięba, C.A. Del Carpio Muñoz, E. Ichiishi, A. Harmalkar, J.J. Gray, A.M.J.J. Bonvin, F. Ambrosetti, R. Vargas Honorato, Z. Jandova, B. Jiménez-García, P.I. Koukos, S. Van Keulen, C.W. Van Noort, M. Réau, J. Roel-Touris, S. Kotelnikov, D. Padhorny, K.A. Porter, A. Alekseenko, M. Ignatov, I. Desta, R. Ashizawa, Z. Sun, U. Ghani, N. Hashemi, S. Vajda, D. Kozakov, M. Rosell, L.A. Rodríguez-Lumbreras, J. Fernandez-Recio, A. Karczynska, S. Grudinin, Y. Yan, H. Li, P. Lin, S. Huang, C. Christoffer, G. Terashi, J. Verburgt, D. Sarkar, T. Aderinwale, X. Wang, D. Kihara, T. Nakamura, Y. Hanazono, R. Gowthaman, J.D. Guest, R. Yin, G. Taherzadeh, B.G. Pierce, D. Barradas-Bautista, Z. Cao, L. Cavallo, R. Oliva, Y. Sun, S. Zhu, Y. Shen, T. Park, H. Woo, J. Yang, S. Kwon, J. Won, C. Seok, Y. Kiyota, S. Kobayashi, Y. Harada, M. Takeda-Shitaka, P.J. Kundrotas, A. Singh, I.A. Vakser, J. Dapkūnas, . Olechnovič, Č. Venclovas, R. Duan, L. Qiu, X. Xu, S. Zhang, X. Zou, S.J. Wodak. Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment. Proteins: Struc. Funct. & Bioinformatics, Advanced Online Publication (2021).

  • R. Vargas Honorato, P.I. Koukos, B. Jimenez-Garcia, A. Tsaregorodtsev, M. Verlato, A. Giachetti, A. Rosato and A.M.J.J. Bonvin. Structural biology in the clouds: The WeNMR-EOSC Ecosystem. Frontiers Mol. Biosci. 8, fmolb.2021.729513 (2021).

  • T Neijenhuis, S.C. van Keulen and A.M.J.J. Bonvin. Interface Refinement of Low-to-Medium Resolution Cryo-EM Complexes using HADDOCK2.4. bioRxiv doi:2021.06.22.449462 (2021).

  • P.I. Koukos, M.F. Reau and A.M.J.J. Bonvin. Shape-restrained modelling of protein-small molecule complexes with HADDOCK. J. Chem. Inf. and Mod. Advanced Online Publication (2021). BioRxiv prepring available here.

  • A.M.J.J. Bonvin. 50 years of PDB: A catalyst in structural biology. Nature Methods 18, 448–449 (2021).

  • C.J. Buchanan, B. Gaunt, P.J. Harrison, A. Le Bas, A. Khan, A.M. Giltrap, P.N. Ward, M. Dumoux, S. Daga, N. Picchiotti, M. Baldassarri, E. Benetti, C. Fallerini, F. Fava, A. Giliberti, P.I. Koukos, A. Lakshminarayanan, X. Xue, G. Papadakis, L.P. Deimel, V. Casablancas-Antràs, T.D.W. Claridge, A.M.J.J. Bonvin, Q.J. Sattentau, S. Furini, M. Gori, J.Huo, R.J. Owens, A. Renieri, GEN-COVID Multicenter Study, J.H. Naismith, A. Baldwin, B.G. Davis. Cryptic SARS-CoV2-spike-with-sugar interactions revealed by ‘universal’ saturation transfer analysis. bioRxiv doi:2021.04.14.439284 (2021).

  • U.B. le Paige, S. Xiang, M.M.R.M. Hendrix, Y. Zhang., G.E. Folkers, M. Weingarth, A.M.J.J. Bonvin, T.G. Kutateladze, I.K.Voets, M. Baldus and H. van Ingen. Characterization of nucleosome sediments for protein interaction studies by solid-state NMR spectroscopy. Magn. Reson., 2, 105-116 (2021).

  • Z. Jandova, A.V. Vargiu and A.M.J.J. Bonvin. Native or non-native protein-protein docking models? Molecular dynamics to the rescue. J. Chem. Theo. and Comp. 17, 5944−5954 (2021).

  • C.W. van Noort, R.V. Honorato and A.M.J.J. Bonvin. Information-Driven Modeling of Biomolecular Complexes. Curr. Opin. Struct. Biol. 70, 70-77 (2021).

  • P. Matos-Filipe, A.J. Preto, P.I. Koukos, J. Mourão, A.M.J.J. Bonvin and I.S. Moreira. MENSADB: A Thorough Structural Analysis of Membrane Protein Dimers. Database, doi:10.1093/database/baab013, 1-10 (2021).

  • N.Renaud, C. Geng, S. Georgievska, F. Ambrosetti, L. Ridder, D.F Marzella, A.M.J.J. Bonvin and L.C. Xue. DeepRank: A deep learning framework for data mining 3D protein-protein interfaces. BioRxiv 10.1101/2021.01.29.425727 (2021)

  • S. Nizamuddin, S. Koidl, T. Bhuiyan, T.V. Werner, M.L. Biniossek, A.M.J.J. Bonvin, S. Lassmann and H.Th.M. Timmers. Integrating quantitative proteomics with accurate genome profiling of transcription factors by greenCUT&RUN. Nucl. Acids Res. 49, e49-‌e49 (2021).

  • O.M.H. Salo-Ahen#, I. Alanko, R. Bhadane, A.M.J.J. Bonvin#, R. Vargas Honorato, S. Hossain, A.H. Juffer, A. Kabedev, M. Lahtela-Kakkonen, A. Støttrup Larsen, E. Lescrinier, P. Marimuthu, M.. Mirza, G. Mustafa, A. Nunes-Alves#, T. Pantsar, A. Saadabadi, K. Singaravelu, M. Vanmeert. Molecular dynamics simulations in drug discovery and pharmaceutical development. Processes. 9, 71 (2021).

  • B. Jiménez-García, J.M.C. Teixeira, M.E. Trellet, J.P.G.L.M. Rodrigues and A.M.J.J. Bonvin. PDB-Tools Web: A user-friendly interface for the manipulation of PDB files Proteins: Struc. Funct. & Bioinformatics, 89, 330-335 (2021).

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1997


  • 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).

1996


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1993


  • 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).

1992


  • 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).

1991


1990