Extended Data Fig. 9: AlphaLink and AlphaFold2 pLDDT correlation.
From: Protein structure prediction with in-cell photo-crosslinking mass spectrometry and deep learning
a- We show the calibration of the predicted lDDT-Cα score (pLDDT) for AlphaLink on N = 220 predictions of the E. coli membrane fraction dataset. On predictions that are at least 80% covered by the crystal structure, the correlation is 0.82. The true lDDT-Cα score is generally underestimated, meaning that the pLDDT-score is a conservative estimate. b- We show the calibration of the predicted lDDT-Cα score (pLDDT) for AlphaFold2 on N = 220 predictions of the E. coli membrane fraction dataset. On predictions that are at least 80% covered by the crystal structure, the correlation is 0.95.The shaded area corresponds to the 95% confidence interval. Line shows the linear fit.
