Extended Data Fig. 10: MSA clusters enable correct predictions for engineered fold-switching point mutations in the protein GA/GB system.
From: Predicting multiple conformations via sequence clustering and AlphaFold2
A) Sequences of the 12 sets of GA/GB point mutations tested, from refs. 49,50,51 Point mutations different from neighbouring sequences in the series are coloured in orange. Right: Representative NMR structures of the GA and GB fold. B) Left: Visualization of sequence identity and coverage of the MSA returned by ColabFold for GA98. Right: Visualization of MSA clusters with more than 10 sequences from the AF-Cluster clustering routine. C) We compared 3 types of MSAs for each point mutation: i) the full MSA returned by ColabFold, ii) MSA clusters returned by AF-Cluster, and iii) MSAs of the wild-type GA and GB proteins in ref. 50 Predictions for which the highest plDDT is incorrect are marked with an X. AF-Cluster has a higher success rate and returns predictions with higher plDDT.
