Alexandre MJJ Bonvin, Ph.D.

Affiliations: 
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 
Area:
Protein-protein interactions, docking
Website:
https://www.uu.nl/staff/amjjbonvin
Google:
"alexandre bonvin"
Bio:

https://www.uu.nl/staff/amjjbonvin/CV

Cross-listing: Neurotree - Chemistry Tree

Parents

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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)

Children

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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)

Collaborators

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Victor L. Hsu collaborator 2005-2005 Utrecht (Physics Tree)
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Publications

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Renaud N, Geng C, Georgievska S, et al. (2021) DeepRank: a deep learning framework for data mining 3D protein-protein interfaces. Nature Communications. 12: 7068
Lensink MF, Brysbaert G, Mauri T, et al. (2021) Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment. Proteins
Koukos PI, Réau M, Bonvin AMJJ. (2021) Shape-Restrained Modeling of Protein-Small-Molecule Complexes with High Ambiguity Driven DOCKing. Journal of Chemical Information and Modeling
Honorato RV, Koukos PI, Jiménez-García B, et al. (2021) Structural Biology in the Clouds: The WeNMR-EOSC Ecosystem. Frontiers in Molecular Biosciences. 8: 729513
Jandova Z, Vargiu AV, Bonvin AMJJ. (2021) Native or Non-Native Protein-Protein Docking Models? Molecular Dynamics to the Rescue. Journal of Chemical Theory and Computation
van Noort CW, Honorato RV, Bonvin AMJJ. (2021) Information-driven modeling of biomolecular complexes. Current Opinion in Structural Biology. 70: 70-77
Bonvin AMJJ. (2021) 50 years of PBD: a catalyst in structural biology. Nature Methods. 18: 448-449
Matos-Filipe P, Preto AJ, Koukos PI, et al. (2021) MENSAdb: a thorough structural analysis of membrane protein dimers. Database : the Journal of Biological Databases and Curation. 2021
Nizamuddin S, Koidl S, Bhuiyan T, et al. (2021) Integrating quantitative proteomics with accurate genome profiling of transcription factors by greenCUT&RUN. Nucleic Acids Research
Schwarz M, Skrinjar P, Fink MJ, et al. (2020) A click-flipped enzyme substrate boosts the performance of the diagnostic screening for Hunter syndrome. Chemical Science. 11: 12671-12676
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