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2020 – today
- 2024
[j27]Anna Ranaudo
, Marco Giulini, Angela Pelissou Ayuso, Alexandre M. J. J. Bonvin:
Modeling Protein-Glycan Interactions with HADDOCK. J. Chem. Inf. Model. 64(19): 7816-7825 (2024)- [i4]Xiaotong Xu, Alexandre M. J. J. Bonvin:
Ranking protein-protein models with large language models and graph neural networks. CoRR abs/2407.16375 (2024) - 2023
- [j26]Manon Réau, Nicolas Renaud, Li C. Xue, Alexandre M. J. J. Bonvin:
DeepRank-GNN: a graph neural network framework to learn patterns in protein-protein interfaces. Bioinform. 39(1) (2023) - 2021
- [j25]Pedro Matos-Filipe, António J. Preto, Panagiotis I. Koukos, Joana Mourão, Alexandre M. J. J. Bonvin, Irina S. Moreira:
MENSAdb: a thorough structural analysis of membrane protein dimers. Database J. Biol. Databases Curation 2021 (2021) - [j24]Panagiotis I. Koukos, Manon Réau, Alexandre M. J. J. Bonvin:
Shape-Restrained Modeling of Protein-Small-Molecule Complexes with High Ambiguity Driven DOCKing. J. Chem. Inf. Model. 61(9): 4807-4818 (2021) - [i3]Rodrigo Vargas Honorato, Panagiotis I. Koukos, Brian Jiménez-García, Andrei Tsaregorodtsev, Marco Verlato, Andrea Giachetti, Antonio Rosato, Alexandre M. J. J. Bonvin:
Structural biology in the clouds: The WeNMR-EOSC Ecosystem. CoRR abs/2107.01056 (2021) - 2020
- [j23]Richard A. Norman, Francesco Ambrosetti, Alexandre M. J. J. Bonvin, Lucy J. Colwell, Sebastian Kelm, Sandeep Kumar, Konrad Krawczyk:
Computational approaches to therapeutic antibody design: established methods and emerging trends. Briefings Bioinform. 21(5): 1549-1567 (2020) - [j22]Cunliang Geng, Yong Jung, Nicolas Renaud, Vasant G. Honavar, Alexandre M. J. J. Bonvin, Li C. Xue:
iScore: a novel graph kernel-based function for scoring protein-protein docking models. Bioinform. 36(1): 112-121 (2020) - [j21]Jorge Roel-Touris, Alexandre M. J. J. Bonvin, Brian Jiménez-García:
LightDock goes information-driven. Bioinform. 36(3): 950-952 (2020) - [j20]Francesco Ambrosetti, Tobias Hegelund Olsen, Pier Paolo Olimpieri, Brian Jiménez-García, Edoardo Milanetti, Paolo Marcatili, Alexandre M. J. J. Bonvin:
proABC-2: PRediction of AntiBody contacts v2 and its application to information-driven docking. Bioinform. 36(20): 5107-5108 (2020) - [j19]Andrea Basciu, Panagiotis I. Koukos, Giuliano Malloci, Alexandre M. J. J. Bonvin, Attilio Vittorio Vargiu:
Coupling enhanced sampling of the apo-receptor with template-based ligand conformers selection: performance in pose prediction in the D3R Grand Challenge 4. J. Comput. Aided Mol. Des. 34(2): 149-162 (2020) - [j18]Nicolas Renaud, Yong Jung, Vasant G. Honavar, Cunliang Geng, Alexandre M. J. J. Bonvin, Li C. Xue:
iScore: An MPI supported software for ranking protein-protein docking models based on a random walk graph kernel and support vector machines. SoftwareX 11: 100462 (2020) - [i2]Caspar van Leeuwen, Damian Podareanu, Valeriu Codreanu, Maxwell X. Cai, Axel Berg, Simon Portegies Zwart, Robin Stoffer, Menno Veerman, Chiel van Heerwaarden, Sydney Otten, Sascha Caron, Cunliang Geng, Francesco Ambrosetti, Alexandre M. J. J. Bonvin:
Deep-learning enhancement of large scale numerical simulations. CoRR abs/2004.03454 (2020)
2010 – 2019
- 2019
- [j17]Anna Vangone, Jörg Schaarschmidt, Panagiotis I. Koukos, Cunliang Geng, Nevia Citro, Mikael E. Trellet, Li C. Xue, Alexandre M. J. J. Bonvin:
Large-scale prediction of binding affinity in protein-small ligand complexes: the PRODIGY-LIG web server. Bioinform. 35(9): 1585-1587 (2019) - [j16]Brian Jiménez-García, Katarina Elez, Panagiotis I. Koukos, Alexandre M. J. J. Bonvin, Anna Vangone:
PRODIGY-crystal: a web-tool for classification of biological interfaces in protein complexes. Bioinform. 35(22): 4821-4823 (2019) - [j15]Panagiotis I. Koukos, Li C. Xue, Alexandre M. J. J. Bonvin:
Protein-ligand pose and affinity prediction: Lessons from D3R Grand Challenge 3. J. Comput. Aided Mol. Des. 33(1): 83-91 (2019) - [j14]Andrea Basciu, Giuliano Malloci, Fabio Pietrucci, Alexandre M. J. J. Bonvin, Attilio Vittorio Vargiu:
Holo-like and Druggable Protein Conformations from Enhanced Sampling of Binding Pocket Volume and Shape. J. Chem. Inf. Model. 59(4): 1515-1528 (2019) - [j13]Mark James Abraham, Rossen Apostolov, Jonathan Barnoud, Paul Bauer, Christian Blau, Alexandre M. J. J. Bonvin, Matthieu Chavent, John D. Chodera, Karmen Condic-Jurkic, Lucie Delemotte, Helmut Grubmüller, Rebecca J. Howard, E. Joseph Jordan, Erik Lindahl, Samuli Ollila, Jana Selent, Daniel G. A. Smith, Phillip J. Stansfeld, Johanna K. S. Tiemann, Mikaël Trellet, Christopher J. Woods, Artem A. Zhmurov:
Sharing Data from Molecular Simulations. J. Chem. Inf. Model. 59(10): 4093-4099 (2019) - 2018
- [j12]Zeynep Kurkcuoglu, Panagiotis I. Koukos, Nevia Citro, Mikael E. Trellet, João P. G. L. M. Rodrigues, Irina S. Moreira, Jorge Roel-Touris, Adrien S. J. Melquiond, Cunliang Geng, Jörg Schaarschmidt, Li C. Xue, Anna Vangone, Alexandre M. J. J. Bonvin:
Performance of HADDOCK and a simple contact-based protein-ligand binding affinity predictor in the D3R Grand Challenge 2. J. Comput. Aided Mol. Des. 32(1): 175-185 (2018) - [i1]João P. G. L. M. Rodrigues, João M. C. Teixeira, Mikaël Trellet, Alexandre M. J. J. Bonvin:
pdb-tools: a swiss army knife for molecular structures. F1000Research 7: 1961 (2018) - 2017
- [j11]Li C. Xue, João P. G. L. M. Rodrigues, Drena Dobbs, Vasant G. Honavar, Alexandre M. J. J. Bonvin:
Template-based protein-protein docking exploiting pairwise interfacial residue restraints. Briefings Bioinform. 18(3): 458-466 (2017) - 2016
- [j10]Li C. Xue, João P. G. L. M. Rodrigues, Panagiotis L. Kastritis, Alexandre M. J. J. Bonvin, Anna Vangone:
PRODIGY: a web server for predicting the binding affinity of protein-protein complexes. Bioinform. 32(23): 3676-3678 (2016) - [j9]Evelyne Deplazes, Josephine Davies, Alexandre M. J. J. Bonvin, Glenn F. King, Alan E. Mark:
Combination of Ambiguous and Unambiguous Data in the Restraint-driven Docking of Flexible Peptides with HADDOCK: The Binding of the Spider Toxin PcTx1 to the Acid Sensing Ion Channel (ASIC) 1a. J. Chem. Inf. Model. 56(1): 127-138 (2016) - 2015
- [j8]G. C. P. van Zundert, Alexandre M. J. J. Bonvin:
DisVis: quantifying and visualizing accessible interaction space of distance-restrained biomolecular complexes. Bioinform. 31(19): 3222-3224 (2015) - 2014
- [j7]Panagiotis L. Kastritis, João P. G. L. M. Rodrigues, Alexandre M. J. J. Bonvin:
HADDOCK2P2I: A Biophysical Model for Predicting the Binding Affinity of Protein-Protein Interaction Inhibitors. J. Chem. Inf. Model. 54(3): 826-836 (2014) - 2012
- [j6]Tsjerk A. Wassenaar, Marc van Dijk, Nuno Loureiro-Ferreira, Gijs van der Schot, Sjoerd Jacob de Vries, Christophe Schmitz, Johan van der Zwan, Rolf Boelens, Andrea Giachetti, Lucio Ferella, Antonio Rosato, Ivano Bertini, Torsten Herrmann, Hendrik R. A. Jonker, Anurag Bagaria, Victor Jaravine, Peter Güntert, Harald Schwalbe, Wim F. Vranken, Jurgen F. Doreleijers, Gert Vriend, Geerten W. Vuister, Daniel Franke, Alexey Kikhney, Dmitri I. Svergun, Rasmus H. Fogh, John M. C. Ionides, Ernest D. Laue, Chris A. E. M. Spronk, Simonas Jurksa, Marco Verlato, Simone Badoer, Stefano Dal Pra, Mirco Mazzucato, Eric Frizziero, Alexandre M. J. J. Bonvin:
WeNMR: Structural Biology on the Grid. J. Grid Comput. 10(4): 743-767 (2012) - [j5]Sjoerd J. L. van Wijk, Adrien S. J. Melquiond, Sjoerd Jacob de Vries, H. Th. Marc Timmers, Alexandre M. J. J. Bonvin:
Dynamic Control of Selectivity in the Ubiquitination Pathway Revealed by an ASP to GLU Substitution in an Intra-Molecular Salt-Bridge Network. PLoS Comput. Biol. 8(11) (2012) - 2011
- [c1]Tsjerk A. Wassenaar, Marc van Dijk, Nuno Loureiro-Ferreira, Gijs van der Schot, Sjoerd Jacob de Vries, Christophe Schmitz, Johan van der Zwan, Rolf Boelens, Andrea Giachetti, Lucio Ferella, Antonio Rosato, Ivano Bertini, Torsten Herrmann, Hendrik R. A. Jonker, Anurag Bagaria, Victor Jaravine, Peter Güntert, Harald Schwalbe, Wim F. Vranken, Jurgen F. Doreleijers, Gert Vriend, Geerten W. Vuister, Daniel Franke, Alexey Kikhney, Dmitri I. Svergun, Rasmus H. Fogh, John M. C. Ionides, Ernest D. Laue, Chris A. E. M. Spronk, Marco Verlato, Simone Badoer, Stefano Dal Pra, Mirco Mazzucato, Eric Frizziero, Alexandre M. J. J. Bonvin:
WeNMR: Structural Biology on the Grid. IWSG-Life 2011 - 2010
- [j4]Mickaël Krzeminski, Karine Loth, Rolf Boelens, Alexandre M. J. J. Bonvin:
SAMPLEX: Automatic mapping of perturbed and unperturbed regions of proteins and complexes. BMC Bioinform. 11: 51 (2010)
2000 – 2009
- 2009
- [j3]Marc van Dijk, Alexandre M. J. J. Bonvin:
3D-DART: a DNA structure modelling server. Nucleic Acids Res. 37(Web-Server-Issue): 235-239 (2009) - 2006
- [j2]Sjoerd Jacob de Vries, Alexandre M. J. J. Bonvin:
Intramolecular surface contacts contain information about protein-protein interface regions. Bioinform. 22(17): 2094-2098 (2006) - [j1]Aalt D. J. van Dijk, Alexandre M. J. J. Bonvin:
Solvated docking: introducing water into the modelling of biomolecular complexes. Bioinform. 22(19): 2340-2347 (2006)
Coauthor Index
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