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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 tried running it on their old site:
https://compbio.soe.ucsc.edu/SAM_T08/T08-query.html
but it is no longer supported :-(
I did love their sequence logos
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.
Should we assume no cysteines pair up to make disulfide bonds?
According to https://fold.it/portal/recipe/43861#comment-28861
and https://fold.it/portal/recipe/43861#comment-41453
for 4 cysteines, there is 1 way to form no disulfide bonds,
6 ways to form 1 disulfide bond, and 3 ways to form 2 disulfide bonds.
From http://clavius.bc.edu/~clotelab/DiANNA/:
Disulfide bond scores
Cys position Distance Bond Score
10 - 41 31 KFLALCADSII-GLYRKCVKSRE 0.01039
10 - 105 95 KFLALCADSII-VGTPVCINGLM 0.01126
10 - 121 111 KFLALCADSII-DTEKYCALAPN 0.01654
41 - 105 64 GLYRKCVKSRE-VGTPVCINGLM 0.01708
41 - 121 80 GLYRKCVKSRE-DTEKYCALAPN 0.01426
105 - 121 16 VGTPVCINGLM-DTEKYCALAPN 0.01097
Step 5: Weighted matching
Predicted bonds
10 - 121 KFLALCADSII - DTEKYCALAPN
41 - 105 GLYRKCVKSRE - VGTPVCINGLM
Predicted connectivity
1-4, 2-3
and from http://disulfind.dsi.unifi.it/monitor.php?query=5oIJ1z
+------------------------------+
| |
.........10........20........30........40........50........60........70........
AA KLVNKFLALCADSIIIGGAKLKALNLGETFVTHSKGLYRKCVKSREETGLLMPLKAPKEIIFLEGETLPTEVLTEEVVL
DB_state 1 1
DB_conf 5 5
+---------------+
| |
80........90........100.......110.......120.......130.......
AA KTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYCALAPNMMVTNNTFTLKGG
DB_state 1 1
DB_conf 6 5
DB_bond bond(10,41)
DB_bond bond(105,121)
Conn_conf 0.749646
Definitions explained here by jeff101: https://fold.it/portal/node/2009630#comment-41525
Thanks Jeff!
Does it mean that there is quite good chances of 2 disulfide bonds (10,41 105,121) ?
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?
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?
My guess is there are very few known proteins with similar sequences. If the algorithm bases its prediction on proteins that are slightly similar but not really related, it can come up with wildly varying SS predictions.
I think this protein only exists inside the host cell - it is probably not packaged into the capsid when the virus exits the cell to travel to a new host. Instead, when outside the cell, it is carried as instructions in the RNA.
0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000001111111111111111111111111111111111111111
0000000001111111111222222222233333333334444444444555555555566666666667777777777888888888899999999990000000000111111111122222222223333333333
1234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789
OrigSeq : KLVNKFLALCADSIIIGGAKLKALNLGETFVTHSKGLYRKCVKSREETGLLMPLKAPKEIIFLEGETLPTEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYCALAPNMMVTNNTFTLKGG : OrigSeq
PsiPred : -HHHHHHHHHHHEEEEE--EEEEEE---EEEEE---EEEEEE--HHHHHHH-------EEEEEE--EE-EEEE--EEEEEEEEEEE----------------EEEE--EEEEEE----EEEEE-----EE--EEEE--- : PsiPred
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 0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000001111111111111111111111111111111111111111
0000000001111111111222222222233333333334444444444555555555566666666667777777777888888888899999999990000000000111111111122222222223333333333
1234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789
OrigSeq : KLVNKFLALCADSIIIGGAKLKALNLGETFVTHSKGLYRKCVKSREETGLLMPLKAPKEIIFLEGETLPTEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYCALAPNMMVTNNTFTLKGG : OrigSeq
PsiPred : LHHHHHHHHHHHEEEEELLEEEEEELLLEEEEELLLEEEEEELLHHHHHHHLLLLLLLEEEEEELLEELEEEELLEEEEEEEEEEELLLLLLLLLLLLLLLLEEEELLEEEEEELLLLEEEEELLLLLEELLEEEELLL : PsiPred
Jnet : LHHHHHHHHHHHHHHHLLLEELLLLLLHHHHHLLLLLEEEEEHLHHEEEEELLLLLLLEEEEELLLLLLEEEEELEEEEEELLLLLLLLLLHHHLLLLEEEEEEEELLLEEEEELLLLLLELLLLLLEEELLEEELLLL : Jnet
jhmm : HHHHHHHHHHHHHHHHLLLEELLLLLLEEEELLLLLLEEEEEELLEEELLLLLLLLLLEEEEELLLLLEEEEEEEEEEEEEEELLLLLLLLLLLLLLLEEEEEEEELLLEEEEELLLLLEEELLLLLEEHHHHHHLLLL : jhmm
jpssm : LHHHHHHHHHHHHHHHHLLLLLLLLHHHHHHHHLLLLHHHHHHHHHHHHHELLLLLLLLEEEELLLLLLHHHHHHHHHHLLLLLLHLHHHHHHHHLLLEEEEEEEELLEEEEEELLLLLLLLLLLLLEEELLEEEELLL : jpssm
I can't seem to open the puzzle, my game crashes every time I try to open it. I know there have been issues in the past with Macs, so I don't know if that's the problem (since I am using a Mac) but I just thought I would mention it.
If 1837 is the puzzle that is crashing for you, open menu, options, and see what the build ID starts with. If it does not start with 20200409, you are running an old version of the game, probably the 32-bit version, which can't handle the new BUNS filter in 1837. If so, you will have to reinstall to get the 64 bit version. Make sure to copy the all.macro and options.txt file out of your game directory before re-installing. Better yet, rename your entire game directory before reinstalling, so you can go get your history (puzzles you have played) out of it later if you want. Reinstalling removes your history.
Better to keep the old version on you Mac, by renaming it.
I tried to re-install (64b) on an old Mac and it didn't work at all. Impossible to come back to the old version of foldit. Since then, I'm running Devprev on the same mac: fortunately I had the old version there. This works very fine but it's impossible to play this BUNS puzzle there, and it doesn't recognise filter or symmetric commands in recent recipes.
An alternative could be to install Linux (Ubuntu) on this Mac, but Linux has it's own problems with Foldit. I've an old PC with linux, but I can only run one client (it was 7 under windows in old times). It's not clear to me if these problems are linked to old computer (defective mastercard) or to system.
wrong puzzle
