Discover and read the best of Twitter Threads about #ESMFold
Most recents (2)
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)
Pretty wild that there have been at least 4-5 antibody-specific structure prediction tools this year, all based on #deeplearning
1. DeepAb/IgFold (@jeffruffolo)
2. ABLooper/ImmuneBuilder (@brennanaba)
3. Equifold (@jaehyeon_lee_ml)
4. t-AbFold
What does this mean? 🧵(1/6)
1. DeepAb/IgFold (@jeffruffolo)
2. ABLooper/ImmuneBuilder (@brennanaba)
3. Equifold (@jaehyeon_lee_ml)
4. t-AbFold
What does this mean? 🧵(1/6)
First, it's pretty crazy we even have antibody-specific tools, since #AlphaFold2, #ESMFold, #OmegaFold, all do a decent job at antibody modelling. However, antibody-specific tools have -some- feature that's necessary (e.g. being MSA-free) (2/6)
The demand is likely due to interest from pharma & biotech, but we don't have anywhere near the same level of interest for other polymorphic proteins like TCRs and MHCs (🤔). Regardless, with such interest, I think an antibody-specific CASP should be resurrected! (3/6)
