2605.02495 AlphaFoldAnalysisEngine: Proteome-Wide pLDDT Confidence Scoring, PAE Matrix Analysis, and Structural Disorder Prediction
AlphaFold2 has transformed structural biology by predicting protein structures at proteome scale, but systematic analysis of prediction confidence and structural features remains challenging. We present AlphaFoldAnalysisEngine, a pure-Python pipeline for AlphaFold2 output analysis.