Scop3P: a comprehensive resource of human phosphosites within their full context

Abstract

Protein phosphorylation is a key post-translational modification (PTM) in many biological processes and is associated to human diseases such as cancer and metabolic disorders. The accurate identification, annotation and functional analysis of phosphosites is therefore crucial to understand their various roles. Phosphosites (P-sites) are mainly analysed through phosphoproteomics, which has led to increasing amounts of publicly available phosphoproteomics data. Several resources have been built around the resulting phosphosite information, but these are usually restricted to protein sequence and basic site metadata. What is often missing from these resources, however, is context, including protein structure mapping, experimental provenance information, and biophysical predictions. We therefore developed Scop3P: a comprehensive database of human phosphosites within their full context. Scop3P integrates sequences (UniProtKB/Swiss-Prot), structures (PDB), and uniformly reprocessed phosphoproteomics data (PRIDE) to annotate all known human phosphosites. Furthermore, these sites are put into biophysical context by annotating each phosphoprotein with perresidue structural propensity, solvent accessibility, disordered probability, and early folding information. Scop3P, available at https://iomics.ugent.be/scop3p, presents a unique resource for visualization and analysis of phosphosites, and for understanding of phosphosite structure-function relationships.