AlphaFold predictions on whole genomes at a glance: a coherent view on packing properties, pLDDT values, and disordered regions

For model organisms, AlphaFold predictions show that 30% to 40% of amino acids have a (very) low pLDDT confidence score. This observation, combined with the method’s high complexity, commands a systematic analysis of AlphaFold predictions on whole genomes. Consequently, using whole-genome predictions, we provide a coherent analysis on packing properties, pLDDT values, and their relationship with intrinsically disordered regions (IDRs). Our contributions are of two kinds. First, we introduce simple and explainable geometrical and topological statistics characterizing predictions. Second, we investigate four key biophysical and biological questions: (i) the clustering of AlphaFold predictions on whole genomes, (ii) the identification of high/low quality predicted domains, (iii) false positive/negative AlphaFold predictions with respect to IDRs, and (iv) the fragmentation of the polypeptide chain in terms of pLDDT values. Altogether, our analysis provide novel insights into AlphaFold predictions across whole genomes, further enhancing the confidence assessment of the models.