DeepRank-GNN: a graph neural network framework to learn patterns in protein–protein interfaces von Réau, Manon, Renaud, Nicolas, Xue, Li C, Bonvin, Alexandre M J J

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A unified conformational selection and induced fit approach to protein-peptide docking von Trellet, Mikael, Melquiond, Adrien S J, Bonvin, Alexandre M J J

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The HADDOCK web server for data-driven biomolecular docking von de Vries, Sjoerd J, van Dijk, Marc, Bonvin, Alexandre M J J

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Distinguishing crystallographic from biological interfaces in protein complexes: role of intermolecular contacts and energetics for classification von Elez, Katarina, Bonvin, Alexandre M J J, Vangone, Anna

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On the binding affinity of macromolecular interactions: daring to ask why proteins interact von Kastritis, Panagiotis L., Bonvin, Alexandre M. J. J.

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DeepRank: a deep learning framework for data mining 3D protein-protein interfaces von Renaud, Nicolas, Geng, Cunliang, Georgievska, Sonja, Ambrosetti, Francesco, Ridder, Lars, Marzella, Dario F., Réau, Manon F., Bonvin, Alexandre M. J. J., Xue, Li C.

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CPORT: a consensus interface predictor and its performance in prediction-driven docking with HADDOCK von de Vries, Sjoerd J, Bonvin, Alexandre M J J

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3D-DART: a DNA structure modelling server von van Dijk, Marc, Bonvin, Alexandre M. J. J.

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Computational approaches to therapeutic antibody design: established methods and emerging trends von Norman, Richard A, Ambrosetti, Francesco, Bonvin, Alexandre M J J, Colwell, Lucy J, Kelm, Sebastian, Kumar, Sandeep, Krawczyk, Konrad

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Integrative modeling of membrane-associated protein assemblies von Roel-Touris, Jorge, Jiménez-García, Brian, Bonvin, Alexandre M. J. J.

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Structural Biology in the Clouds: The WeNMR-EOSC Ecosystem von Honorato, Rodrigo V., Koukos, Panagiotis I., Jiménez-García, Brian, Tsaregorodtsev, Andrei, Verlato, Marco, Giachetti, Andrea, Rosato, Antonio, Bonvin, Alexandre M. J. J.

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Pre‐ and post‐docking sampling of conformational changes using ClustENM and HADDOCK for protein‐protein and protein‐DNA systems von Kurkcuoglu, Zeynep, Bonvin, Alexandre M. J. J.

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Antimicrobial and efflux pump inhibitory activity of caffeoylquinic acids from Artemisia absinthium against gram-positive pathogenic bacteria von Fiamegos, Yiannis C, Kastritis, Panagiotis L, Exarchou, Vassiliki, Han, Haley, Bonvin, Alexandre M J J, Vervoort, Jacques, Lewis, Kim, Hamblin, Michael R, Tegos, George P

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Plectasin, a Fungal Defensin, Targets the Bacterial Cell Wall Precursor Lipid II von Schneider, Tanja, Kruse, Thomas, Wimmer, Reinhard, Wiedemann, Imke, Sass, Vera, Pag, Ulrike, Jansen, Andrea, Nielsen, Allan K, Mygind, Per H, Raventós, Dorotea S, Neve, Søren, Ravn, Birthe, Bonvin, Alexandre M.J.J, De Maria, Leonardo, Andersen, Anders S, Gammelgaard, Lora K, Sahl, Hans-Georg, Kristensen, Hans-Henrik

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Structure and Flexibility Adaptation in Nonspecific and Specific Protein-DNA Complexes von Kalodimos, Charalampos G., Biris, Nikolaos, Alexandre M. J. J. Bonvin, Levandoski, Marc M., Guennuegues, Marc, Boelens, Rolf, Kaptein, Robert

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Sequence co-evolution gives 3D contacts and structures of protein complexes von Hopf, Thomas A, Schärfe, Charlotta P I, Rodrigues, João P G L M, Green, Anna G, Kohlbacher, Oliver, Sander, Chris, Bonvin, Alexandre M J J, Marks, Debora S

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SpotOn: High Accuracy Identification of Protein-Protein Interface Hot-Spots von Moreira, Irina S., Koukos, Panagiotis I., Melo, Rita, Almeida, Jose G., Preto, Antonio J., Schaarschmidt, Joerg, Trellet, Mikael, Gümüş, Zeynep H., Costa, Joaquim, Bonvin, Alexandre M. J. J.

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Mode of action of teixobactins in cellular membranes von Shukla, Rhythm, Medeiros-Silva, João, Parmar, Anish, Vermeulen, Bram J. A., Das, Sanjit, Paioni, Alessandra Lucini, Jekhmane, Shehrazade, Lorent, Joseph, Bonvin, Alexandre M. J. J., Baldus, Marc, Lelli, Moreno, Veldhuizen, Edwin J. A., Breukink, Eefjan, Singh, Ishwar, Weingarth, Markus

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Are Scoring Functions in Protein−Protein Docking Ready To Predict Interactomes? Clues from a Novel Binding Affinity Benchmark von Kastritis, Panagiotis L, Bonvin, Alexandre M. J. J

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iScore: a novel graph kernel-based function for scoring protein–protein docking models von Geng, Cunliang, Jung, Yong, Renaud, Nicolas, Honavar, Vasant, Bonvin, Alexandre M J J, Xue, Li C

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