Fold this coronavirus protein! This is the tail portion of a larger protein encoded in the viral genome of SARS-CoV-2. It is encoded in a region of the genome called NSP2, but the protein's structure and function are still unknown. If we knew how this protein folds, we might be able to figure out its exact function. The puzzle's starting structure shows SS predictions from PSIPRED, and hints which parts of the protein might fold into helices or sheets. Refold this protein to find high-scoring solutions, which will tell us how this protein is most likely to fold!
Do you know what software the SAM-T08 server ran for predictions ? I think a plot like that would be infinitely more helpful with this beautiful disaster.
I did as well, I really made it a lot easier when deciding when and where to make changes. I have been downloading different software to play with, but have not found anything close to it.
I ran the Jpred prediction and something is very strange with this protein. I have never before seen that the 3 engines they use have very different outcomes. One is really different.
OrigSeq : KLVNKFLALCADSIIIGGAKLKALNLGETFVTHSKGLYRKCVKSREETGLLMPLKAPKEIIFLEGETLPTEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYCALAPNMMVTNNTFTLKGG : OrigSeq
Jnet : -HHHHHHHHHHHHHHH—EE——HHHHH—–EEEEEH-HHEEEEE——-EEEEE——EEEEE-EEEEEE———-HHH—-EEEEEEEE—EEEEE——E——EEE–EEE—- : Jnet
jhmm : HHHHHHHHHHHHHHHH—EE——EEEE——EEEEEE–EEE———-EEEEE—–EEEEEEEEEEEEEEE—————EEEEEEEE—EEEEE—–EEE—–EEHHHHHH—- : jhmm
jpssm : -HHHHHHHHHHHHHHHH——–HHHHHHHH—-HHHHHHHHHHHHHE——–EEEE——HHHHHHHHHH——H-HHHHHHHH—EEEEEEEE–EEEEEE————-EEE–EEEE— : jpssm
As you can see the jpssm prediction has way more helices as the other 2. Can it be that this is a protein with 2 structures, one inside the virus and one when it enters or is inside a cell?
