Vincent Zoete

Rapid and Reliable Structural Modeling of Adaptive Immune Receptors Using an Optimized AlphaFold3 workflow

This paper optimizes AlphaFold3 for rapid and reliable structural modeling of antibodies and T-cell receptors, achieving 45-fold faster MSA phase and 3.6-fold faster inference.

Attracting Cavities 3.0: Faster and More Versatile Molecular Docking for the SwissDock Webserver

The paper improves the molecular docking algorithm Attracting Cavities, enhancing its speed, sampling, and versatility while demonstrating better performance compared to AutoDock Vina.

Comparative Assessment of the Utility of Co-Folding and Docking for Small-Molecule Drug Design

This study compares co-folding and docking methods for drug design, finding that physics-based docking outperforms co-folding for novel ligands and provides physical rationale for binding.

Novel universal domain-centric method for protein classification

The paper introduces a domain-centric method using physico-chemical properties to classify proteins, improving accuracy over traditional phylogeny-based approaches.

Knowledge-guided machine-learning and reverse screening combined method to predict cancer cell line responses to cytotoxic molecules

The paper develops a method combining machine learning and reverse screening to predict cancer cell line responses to cytotoxic molecules, achieving 71% accuracy in identifying experimental targets.

Rethinking Molecular Beauty in the Deep Learning Era

This paper introduces OiiSTER-map, a 2D heatmap to evaluate molecular quality in generative chemistry by combining bioactivity and structural features, aiming to improve drug discovery assessment.

Key determinants of T cell epitope recognition revealed by TCR specificity profiles

The paper introduces TCR specificity profiles to identify key determinants of TCR-epitope recognition and shows their ability to predict cross-reactivity and interpret machine learning models.

Phage display enables machine learning discovery of cancer antigen specific TCRs

The paper uses phage display and machine learning to discover TCRs specific to cancer antigens, identifying functional TCRs from large repertoires.

Redirecting TCR specificity in regulatory T cells toward class I HLA antigens mediates tissue-specific homing

The paper redirects TCR specificity in regulatory T cells toward class I HLA antigens to enhance tissue-specific homing in Type 1 Diabetes.

Dominant monoallelic variant in the PAK2 gene causes Knobloch syndrome type 2

The paper identifies a dominant monoallelic PAK2 variant causing Knobloch syndrome type 2 with intellectual disability and retinal degeneration.