We compared rigid docking with varying prior knowledge to AF3 on single-ligand systems in RnP. Unrealistic scenario (redocking) shows cases in lower bins aren’t challenging from a physics perspective, while AF3-dock-ideal indicates holo conformation prediction for those cases remains difficult.(2/5)
Interestingly, Boltz1x shows similar success rate compared to Boltz-1, but has a boost in PB-valid predictions (F), with all predicted systems passing the Minimum Distance To Protein check, which seems to be a major issue for other methods (E). (4/5)
Meanwhile, Boltz-2 was released (cutoff 1 June 2023), using ~2 extra years of PDB data vs others. This additional data does not seem to improve generalization with the current architecture (a) and also significantly decreases the number of difficult systems in the RnP (b). (3/5)
Now published in NSMB!
Paper: doi.org/10.1038/s415...
Full PDF: rdcu.be/fhBtI
Overview of additions since the preprint👇 (1/5)
Thanks again to the co-authors @jeeberhardt.bsky.social, @torstenschwede.bsky.social, @ninjani.bsky.social and all collaborators! It’s great to see our work being widely used to benchmark and improve new methods (e.g., OpenFold3, Isomorphic Labs, Pearl), helping advance the field of PLI prediction!
