Bonvin, Alexandre M. J. J.

HADDOCK: A Protein−Protein Docking Approach Based on Biochemical or Biophysical Information

Dominguez, C., Boelens, R., & Bonvin, A. M. J. J. (2003) · Journal of the American Chemical Society

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 3,187

The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes

van Zundert, G. C. P., Rodrigues, J. P. G. L. M., Trellet, M., Schmitz, C., Kastritis, P. L., Karaca, E., Melquiond, A. S. J., van Dijk, M., de Vries, S. J., & Bonvin, A. M. J. J. (2016) · Journal of Molecular Biology

Protein Structure and DynamicsComputational Drug Discovery Methods

Cited by 2,785

Structure and Flexibility Adaptation in Nonspecific and Specific Protein-DNA Complexes

Kalodimos, C. G., Biris, N., Bonvin, A. M. J. J., Levandoski, M. M., Guennuegues, M., Boelens, R., & Kaptein, R. (2004) · Science

Diffusion and Search DynamicsProtein Structure and Dynamics

Cited by 543

Sequence co-evolution gives 3D contacts and structures of protein complexes

Hopf, T. A., Schärfe, C. P. I., Rodrigues, J. P. G. L. M., Green, A. G., Kohlbacher, O., Sander, C., Bonvin, A. M. J. J., & Marks, D. S. (2014) · eLife

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 515

Structural basis for signal-sequence recognition by the translocase motor SecA as determined by NMR.

Gelis, I., Bonvin, A. M. J. J., Keramisanou, D., Koukaki, M., Gouridis, G., Karamanou, S., Economou, A., & Kalodimos, C. G. (2007) · Cell

Bacterial Genetics and BiotechnologyProtein Structure and Dynamics

Cited by 433

Updates to the integrated protein-protein interaction benchmarks: docking benchmark version 5 and affinity benchmark version 2

Vreven, T., Moal, I. H., Vangone, A., Pierce, B. G., Kastritis, P. L., Torchala, M., Chaleil, R., Jiménez-García, B., Bates, P. A., Fernandez-Recio, J., et al. (2015) · Journal of Molecular Biology

Protein Structure and DynamicsComputational Drug Discovery Methods

Cited by 424

Computational approaches to therapeutic antibody design: established methods and emerging trends

Norman, R. A., Ambrosetti, F., Bonvin, A. M. J. J., Colwell, L. J., Kelm, S., Kumar, S., & Krawczyk, K. (2020) · Briefings in Bioinformatics

Monoclonal and Polyclonal Antibodies Researchvaccines and immunoinformatics approaches

Cited by 219

Teixobactin kills bacteria by a two-pronged attack on the cell envelope

Shukla, R., Lavore, F., Maity, S., Derks, M. G. N., Jones, C. R., Vermeulen, B. J. A., Melcrová, A., Morris, M. A., Becker, L. M., Wang, X., et al. (2022) · Nature

Antimicrobial Peptides and ActivitiesAntimicrobial agents and applications

Cited by 201

DeepRank-GNN: a graph neural network framework to learn patterns in protein–protein interfaces

Réau, M., Renaud, N., Xue, L. C., & Bonvin, A. M. J. J. (2023) · Bioinformatics

Computational Drug Discovery MethodsProtein Structure and Dynamics

Cited by 190

DeepRank-GNN: A Graph Neural Network Framework to Learn Patterns in Protein-Protein Interfaces

Réau, M., Renaud, N., Xue, L. C., & Bonvin, A. M. J. J. (2021) · Bioinformatics

Computational Drug Discovery MethodsProtein Structure and Dynamics

Cited by 190

Assessment of contact predictions in CASP12: Co‐evolution and deep learning coming of age

Schaarschmidt, J., Monastyrskyy, B., Kryshtafovych, A., & Bonvin, A. M. J. J. (2018) · Proteins: Structure, Function, and Bioinformatics

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 177

A comprehensive framework of E2-RING E3 interactions of the human ubiquitin-proteasome system

van Wijk, S. J. L., de Vries, S. J., Kemmeren, P., Huang, A., Boelens, R., Bonvin, A. M. J. J., & Timmers, H. T. M. (2009) · Molecular Systems Biology

Ubiquitin and proteasome pathwaysProtein Degradation and Inhibitors

Cited by 164

Dynamic binding mode of a Synaptotagmin-1–SNARE complex in solution

Brewer, K. D., Bacaj, T., Cavalli, A., Camilloni, C., Swarbrick, J. D., Liu, J., Zhou, A., Zhou, P., Barlow, N., Xu, J., et al. (2015) · Nature Structural & Molecular Biology

Cellular transport and secretionNeuroscience and Neuropharmacology Research

Cited by 142

DeepRank: a deep learning framework for data mining 3D protein-protein interfaces

Renaud, N., Geng, C., Georgievska, S., Ambrosetti, F., Ridder, L., Marzella, D. F., Réau, M. F., Bonvin, A. M. J. J., & Xue, L. C. (2021) · Nature Communications

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 125

Blind prediction of homo- and hetero-protein complexes: the CASP13-CAPRI experiment

Lensink, M. F., Brysbaert, G., Nadzirin, N., Velankar, S., Chaleil, R. A. G., Gerguri, T., Bates, P. A., Laine, E., Carbone, A., Grudinin, S., et al. (2019) · Proteins Structure Function and Bioinformatics

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 122

SpotOn: High Accuracy Identification of Protein-Protein Interface Hot-Spots

Moreira, I. S., Koukos, P. I., Melo, R., Almeida, J. G., Preto, A. J., Schaarschmidt, J., Trellet, M., Gümüş, Z. H., Costa, J., & Bonvin, A. M. J. J. (2017) · Scientific Reports

Machine Learning in BioinformaticsProtein Structure and Dynamics

Cited by 98

iSEE: Interface structure, evolution, and energy-based machine learning predictor of binding affinity changes upon mutations

Geng, C., Vangone, A., Folkers, G. E., Xue, L. C., & Bonvin, A. M. J. J. (2019) · Proteins: Structure, Function, and Bioinformatics

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 82

Travel-driven emergence and spread of SARS-CoV-2 lineage B.1.620 with multiple VOC-like mutations and deletions in Europe

Dudas, G., Hong, S. L., Potter, B., Calvignac-Spencer, S., Niatou-Singa, F. S., Tombolomako, T. B., Fuh-Neba, T., Vickos, U., Ulrich, M., Leendertz, F. H., et al. (2021) · Nature Communications

SARS-CoV-2 and COVID-19 ResearchCOVID-19 epidemiological studies

Cited by 76

HADDOCK3: A modular and versatile platform for integrative modelling of biomolecular complexes

Giulini, M., Reys, V., Teixeira, J. M. C., Jiménez-García, B., Honorato, R. V., Kravchenko, A., Xu, X., Versini, R., Engel, A., Verhoeven, S., et al. (2025) · Journal of Chemical Information and Modeling

Protein Structure and DynamicsComputational Drug Discovery Methods

Cited by 51

HADDOCK3: A Modular and Versatile Platform for Integrative Modeling of Biomolecular Complexes

Giulini, M., Reys, V., Teixeira, J. M. C., Jiménez-García, B., V. Honorato, R., Kravchenko, A., Xu, X., Versini, R., Engel, A., Verhoeven, S., et al. (2025) · Journal of Chemical Information and Modeling

Protein Structure and DynamicsComputational Drug Discovery Methods

Cited by 51

Towards the accurate modelling of antibody−antigen complexes from sequence using machine learning and information-driven docking

Giulini, M., Schneider, C., Cutting, D., Desai, N., Deane, C. M., & Bonvin, A. M. J. J. (2024) · Bioinformatics

Protein Structure and Dynamicsvaccines and immunoinformatics approaches

Cited by 41

Towards the accurate modelling of antibody-antigen complexes from sequence using machine learning and information-driven docking

Giulini, M., Schneider, C., Cutting, D., Desai, N., Deane, C. M., & Bonvin, A. M. J. J. (2023) · Bioinformatics

Protein Structure and Dynamicsvaccines and immunoinformatics approaches

Cited by 41

DeepRank-GNN-esm: A Graph Neural Network for Scoring Protein-Protein Models using Protein Language Model

Xu, X., & Bonvin, A. M. J. J. (2023) · Bioinformatics Advances

Protein Structure and DynamicsComputational Drug Discovery Methods

Cited by 37

Pre- and post-docking sampling of conformational changes using ClustENM and HADDOCK for protein-protein and protein-DNA systems

Kurkcuoglu, Z., & Bonvin, A. M. J. J. (2020) · Proteins Structure Function and Bioinformatics

Protein Structure and DynamicsComputational Drug Discovery Methods

Cited by 37