AlphaFold and Protein Design
Key Gotchas
- AF2 does not predict dynamics — single static conformation, typically most stable
- High pLDDT ≠ biologically correct — disordered regions can predict high pLDDT if they resemble structured training data
- PAE is directional: PAE[i,j] asks "if residue i is placed correctly, how confident about j?" — not symmetric
- AF2 vs AF3: AF2 is for single proteins/homomers. AF3 handles protein-DNA, protein-RNA, protein-ligand, modified resid
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