Robbie P. Joosten

AlphaBridge evaluates predicted biomolecular complexes using AlphaFold3 confidence metrics, clustering sequence motifs, and visualizing interfaces with 2D diagrams and interactive tools.

The paper analyzes halogen bonds in protein-ligand complexes using geometric parameters and introduces a score to assess their validity in structure models from PDB-REDO.

The paper describes how Foldit players improved protein structure models in the PDB, enhancing the output of the PDB-REDO pipeline.

The paper introduces In-Pocket, a computational method that validates and improves the chemical accuracy of protein-ligand binding interfaces using quantum mechanics and experimental data.

DSSP 4 annotates protein secondary structure in a FAIR-compliant manner, introducing left-handed κ-helices and improving interoperability with mmCIF format.

This study identifies Caskin2 as a novel talin-binding protein that enhances cell motility through interactions with Abi1 and the WAVE Regulatory Complex.

AlphaFill adds missing ligands and cofactors to AlphaFold protein models using sequence and structure similarity to improve functional interpretation.

3D-Beacons provides a federated network to unify access to protein structure data from multiple sources, enabling comparative analysis of models.

The paper presents methods to complete missing regions in protein structures using homology information, resulting in 24,962 completed loops in the PDB.