Secondary structure prediction

HADDOCK
1

Hi guys,
I am trying to predict a secondary structure of a 35-aa long peptide. So far, I tried Spider, Jpred and PSIpred servers. All of them are based on the PSI-Blast alignment. For my purpose, I need to predict the secondary structure without PSI-Blast alignment, just based on the aminoacid sequence. Or at least, the possibility to avoid some PDB during the alignment. Do you have suggestion/comment on this?
Thanks
Best
andrea

2

Hi Andrea,

Maybe you can take a look at CABSfold, it can be used de novo if I remember well

Cheers
Adrien

3

Thanks! I will have look to it