I have a peptide X of length 50aa. Alphafold2 predicted the structure which takes a helix form and with high average pLDDT score (>90).

But during actual experiment (e.g. crystallography, spectroscopy), peptide X is determined to have a random coil structure.

My question is how can I resolve the difference between AF2 prediction and crystallography? To what extend we can use AF2 peptide structure prediction for downstream analysis (e.g. docking, etc)?

  • $\begingroup$ I gave my +1 long ago, and even tried to help get this answered by asking an AlphaFold expert, but got the response "I am not surprised such a vague question gets no answers. Crystallography doesn't show structures have random coil structure -- maybe that means they weren't able to crystallize it." Are you able to make it less vague? Alternatively, maybe you figured out the answer to your question or don't need it as much anymore? Let us know! Also the title should say "Alphafold 2" rather than "Alphafold2", not only because that's how DeepMind typesets it, but because... $\endgroup$ Nov 1, 2022 at 21:57
  • $\begingroup$ ... I couldn't find this question when searching for the "Alphafold" questions. Apparently "Alphafold2" isn't a good enough match for StackExchange's search engine! $\endgroup$ Nov 1, 2022 at 21:57


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