Hello,
I would like to know if distance constrains, such as information about cross-linking lysines within a protein can affect the prediction of secondary structure.
I am refering to my recent protein prediction results for a protein lprF (job IDs S152112 and S152257). In one case (S152257), I did not use distance constrain while for the job ID S152112, I use distance constrain formation (DIST 71 CA 27 CA 20.0 , DIST 204 CA 112 CA 20.0). The top two models for the two jobs were highly similar for most of the protein sequence, except for a small N-terminal peptide (between 47-50 aa residue). The model generated using the distance constrains ( S152112) showed beta sheet as a secondary structure for that region while the model without the constrains did not show any secondary structure.
Cold you please explain this difference?
Thank you,
Arti