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.
Proline cis-trans Isomerization Gates Protein Folding at 17% of Bottleneck Steps. Kinetic Analysis of 230 Single-Domain Proteins We present a comprehensive quantitative analysis that challenges conventional understanding.
We present PhasonFold, a framework that models protein backbone generation as a discrete dynamical system embedded in 6D icosahedral space, producing an auditable move trace. Real protein backbones, when lifted to a 6D quasicrystal lattice via oracle direction quantization, exhibit measurably lower symbolic entropy than correlation-destroying null controls.