Alexandre MJJ Bonvin, Ph.D.

1989-1994 Chemistry Utrecht University, Utrecht, Netherlands 
 1994-1996 Molecular Biophysics and Biochemistry Yale University, New Haven, CT 
 1996-1998 Physical Chemistry Eidgenössische Technische Hochschule Zürich, Zürich, ZH, Switzerland 
 1998- Chemistry Utrecht University, Utrecht, Netherlands 
Protein-protein interactions, docking
"alexandre bonvin"

Cross-listing: Neurotree - Chemistry Tree


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Rolf Boelens grad student 1993 Utrecht (Neurotree)
Robert Kaptein grad student 1993 Utrecht (Chemistry Tree)
 (Determination of biomolecular structures by NMR. Use of relaxation matrix calculations)
Axel Brunger post-doc Yale (Chemistry Tree)
Wilfred F. van Gunsteren research scientist 1996-1998 ETH Zürich (Physics Tree)


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Charlotte van Noort grad student 2019- Utrecht (Neurotree)
Cyril Dominguez grad student 2000-2004 Utrecht (Chemistry Tree)
Shang-Te Danny Hsu grad student 2000-2005 Utrecht (Neurotree)
Aalt-Jan van Dijk grad student 2002-2006 Utrecht (Neurotree)
Marc van Dijk grad student 2004-2009 Utrecht (Neurotree)
Mickaël Krzeminski grad student 2004-2009 Utrecht (Neurotree)
Sjoerd De Vries grad student 2005-2010 Utrecht (Neurotree)
Panagiotis L. Kastritis grad student 2008-2012 Utrecht (Neurotree)
Ezgi Karaca grad student 2008-2013 Utrecht (Chemistry Tree)
João PGLM Rodrigues grad student 2010-2014 Utrecht (Chemistry Tree)
Gydo van Zundert grad student 2012-2016 Utrecht (Neurotree)
Cunliang Geng grad student 2014-2018 Utrecht (Neurotree)
Panagiotis Koukos grad student 2016-2020 Utrecht (Neurotree)
Francesco Ambrosetti grad student 2017-2020 Utrecht (Neurotree)
Jorge Roel Touris grad student 2017-2021 Utrecht (Neurotree)
Zeynep Kurkcuoglu post-doc 2015- Utrecht (Neurotree)
Rodrigo Vargas Honorato post-doc 2019- Utrecht (Neurotree)
Manon Reau post-doc 2020- Utrecht (Neurotree)
Gloria Fuentes post-doc 2002-2006 (Chemistry Tree)
Aurelien Thureau post-doc 2005-2006 Utrecht (Neurotree)
Jeff Grinstead post-doc 2004-2007 Utrecht (Neurotree)
Ludovic Carlier post-doc 2007-2008 Utrecht (Neurotree)
Tsjerk Wassenaar post-doc 2006-2009 Utrecht (Neurotree)
Nuno L. Ferreira post-doc 2008-2010 Utrecht (Neurotree)
Christian Koehler post-doc 2009-2010 Utrecht (Neurotree)
Alexey Neumoin post-doc 2009-2010 Utrecht (Neurotree)
Dirk Straatman post-doc 2009-2010 Utrecht (Neurotree)
Christophe Schmitz post-doc 2010-2012 Utrecht (Neurotree)
Adrien SJ Melquiond post-doc 2007-2013 Utrecht (Neurotree)
Anna Vangone post-doc 2013-2017 Utrecht (Neurotree)
Irina Moreira post-doc 2016-2018 Utrecht (Neurotree)
Joerg Schaarschmidt post-doc 2016-2018 Utrecht (Neurotree)
Mikael Trellet post-doc 2016-2019 Utrecht (Neurotree)
Attilio Vargiu post-doc 2018-2019 Utrecht (Neurotree)
Zuzana Jandova post-doc 2019-2020 Utrecht (Physics Tree)
Brian Jimenez Garcia post-doc 2018-2021 Utrecht (Neurotree)
Li Xue research scientist 2015-2019 Utrecht (Neurotree)


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Victor L. Hsu collaborator 2005-2005 Utrecht (Physics Tree)
BETA: Related publications


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Basciu A, Malloci G, Koukos P, et al. (2020) EDES: A Protocol to Generate Holo-Like and Druggable Protein Conformations Starting from the APO Structure Biophysical Journal. 118: 44a
Geng C, Narasimhan S, Rodrigues JP, et al. (2017) Information-Driven, Ensemble Flexible Peptide Docking Using HADDOCK. Methods in Molecular Biology (Clifton, N.J.). 1561: 109-138
van Zundert GC, Trellet M, Schaarschmidt J, et al. (2016) The DisVis and PowerFit web servers: Explorative and Integrative Modeling of Biomolecular Complexes. Journal of Molecular Biology
de Bruin RC, Stam AG, Vangone A, et al. (2016) Prevention of Vγ9Vδ2 T Cell Activation by a Vγ9Vδ2 TCR Nanobody. Journal of Immunology (Baltimore, Md. : 1950)
Vangone A, Rodrigues JP, Xue LC, et al. (2016) Sense and Simplicity in HADDOCK Scoring: Lessons from CASP-CAPRI Round1. Proteins
Spiliotopoulos D, Kastritis PL, Melquiond AS, et al. (2016) dMM-PBSA: A New HADDOCK Scoring Function for Protein-Peptide Docking. Frontiers in Molecular Biosciences. 3: 46
Xue LC, Rodrigues JP, Kastritis PL, et al. (2016) PRODIGY: a web server for predicting the binding affinity of protein-protein complexes. Bioinformatics (Oxford, England)
Melo R, Fieldhouse R, Melo A, et al. (2016) A Machine Learning Approach for Hot-Spot Detection at Protein-Protein Interfaces. International Journal of Molecular Sciences. 17
Geng C, Vangone A, Bonvin AM. (2016) Exploring the interplay between experimental methods and the performance of predictors of binding affinity change upon mutations in protein complexes. Protein Engineering, Design & Selection : Peds
Liu Y, Rodrigues JP, Bonvin AM, et al. (2016) New insight in the catalytic mechanism of bacterial MraY from enzyme kinetics and docking studies. The Journal of Biological Chemistry
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