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Ran some experiments! #ImmuneBuilder is better than #ESMFold (@alexrives / @TomSercu), right? There are advantages of using the latter, and now a 🧵 on why getting carried away with low RMSDs is only a part of the story...(1/5)
#machinelearning #proteins
#machinelearning #proteins
First, the metrics are RMSDs based on aligning the C/N/CA/CB atoms across the chain, then calculating the RMSD across a region. i.e. align every residue of the VH, then calculate RMSD across CDRH3, or CDRH1, etc. This is on ~35 antibodies of the ImmuneBuilder test set (2/5)
ESMFold's CDRH3 accuracies are better than what I expected. Where it's let down is on the "canonical" CDRs. It would've been nice to compare the VH-VL orientations and talk about how ImmuneBuilder doesn't generate D-amino acids, etc. (3/5)
