Characterizing the fragmentation of AlphaFold predictions

Abstract The Nobel prize winning program AlphaFold computes plausible structures of (well) folded proteins. The main quality assessment is based on the predicted Local Distance Difference Test (pLDDT), a per amino acid confidence score. To enhance quality assessment, we provide novel quantitative measures to identify coherent amino acid (a.a.) stretches along the sequence in terms of pLDDT values. These measures, which rely on standard tools from topological data analysis and combinatorics, qualify the coherence / fragmentation of AlphaFold predictions. The outcome of our analysis can readily be used to select reliable regions/domains within proteins whose pLDDT values span the entire pLDDT range.