CLUMPS-PTM
3D-structural clustering of post-translational modifications
An algorithm for identifying statistically significant 3D clusters of post-translational modifications (PTMs) on protein structures. CLUMPS-PTM maps phosphorylation, acetylation, ubiquitination, and other modification sites onto 3D protein structures to detect spatial enrichment, helping to nominate functionally important regulatory hotspots. It was applied across the CPTAC pan-cancer cohorts in (Geffen et al., 2023), and used to identify PTM-associated structural clusters in the CPTAC lung adenocarcinoma cohort in (Satpathy et al., 2025).