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Status: Unchecked ×Keyword: protein conformational diversity ×Clear all

2 claims from 1 paper

1. Biochemistry, Genetics and Molecular Biology › Protein Structure and Dynamics

   Impact of protein conformational diversity on AlphaFold predictions

   Saldaño, Escobedo, Marchetti et al. · Bioinformatics · 2022

   The paper tested AlphaFold2, run through ColabFold, on apo–holo pairs of protein conformers and examined how well it handles proteins that exist as ensembles of shapes.

   Unchecked2 claims
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   1. UncheckedAlphaFold2's predictions became less accurate for proteins that adopt a wider range of shapes (greater conformational diversity), as the paper reports.“More importantly, we found that AlphaFold2's performance worsens with the increasing conformational diversity of the studied protein.”
   2. UncheckedIn AlphaFold2 models, regions that flex more between ligand-free and ligand-bound forms tend to have lower plDDT, a per-residue confidence score.“Finally, we found that main-chain flexibility associated with apo–holo pairs of conformers negatively correlates with the predicted local model quality score plDDT, indicating that plDDT values in a single 3D model could be used to infer local conformational changes linked to ligand binding transit…”