Jacob C. Verburgt

This paper evaluates blind predictions of dynamic water and ion ensembles around RNA using cryo-EM densities from CASP16, finding that molecular dynamics approaches perform best.

This paper improves AlphaFold's self-confidence scoring by modifying its LDDT prediction head to provide more accurate model quality assessments.

DistPepFold improves protein-peptide complex docking using a privileged knowledge distillation approach based on AlphaFold-Multimer, outperforming AFM on two datasets.

The paper analyzes SARS-CoV-2 spike glycoprotein sequences to show that indels are common and increasing, with implications for viral evolution and vaccine efficacy.