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)?