Author
Utrecht UniversityORCID 0009-0006-1883-6692Unclaimed ORCID profile · follow to get notified of new preprints
Mutual co-authors in cluster
6 papers
Recent·Most cited
Xiaotong Xu, Alexandre M. J. J. Bonvin
AbTune improves protein language model performance for antibody-related tasks through depth-selective fine-tuning, outperforming baselines in structure prediction and mutation effect prediction.
Xiaotong Xu, Ilaria Coratella, Victor Reys, Alexandre M. J. J. Bonvin
DeepRank-Ab improves scoring of antibody-antigen complexes using geometric deep learning, outperforming existing methods in accuracy and ranking.
Marco Giulini, Victor Reys, João M. C. Teixeira…·Alexandre M. J. J. Bonvin
HADDOCK3 is a new modular platform for integrative biomolecular complex modelling, offering enhanced flexibility and integration with third-party tools to complement machine learning predictions.
Marco Giulini, Xiaotong Xu, Alexandre M. J. J. Bonvin
The paper improves antibody structure prediction by combining AlphaFlow and HADDOCK to generate diverse CDR-H3 loop conformations, enhancing docking accuracy for antibody-antigen complexes.
Victor Reys, Marco Giulini, Vlad Cojocaru…·Alexandre M. J. J. Bonvin
The paper summarizes HADDOCK's performance in CAPRI rounds 47-55, highlighting the effectiveness of integrating HADDOCK with AI-driven methods like AlphaFold2 for protein complex structure prediction.
Xiaotong Xu, Alexandre M. J. J. Bonvin
This paper introduces DeepRank-GNN-esm, a graph neural network that uses ESM-2 embeddings to score protein-protein models, replacing computationally expensive PSSM features and improving performance on docking and crystal artifact detection tasks.