Improved protein complex prediction with AlphaFold-multimer by denoising the MSA profile
Fig 2
a) MMscores of difficult targets that have low ranking confidence (RC, Eq 1) (n = 487) with AF-multimer compared to AFProfile. In total, 33% of the failed examples can be rescued and selected (MMscore>0.75 and RC>0.8) with AFProfile. b) MMscore vs confidence. The density represents all predictions (100 per target, n = 48700) and the line is the running mean using a step size of 0.01 confidence. c) Density plot of the confidence vs iteration of gradient descent with AFProfile (n = 48700). At higher iterations, there is a strong density of high confidence. Following Fig 2B, this region is more likely to have high MMscores.