How to specify secondary structure on downloaded I-TASSER?

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DavidB256
Posts: 4
Joined: Fri Jun 11, 2021 4:01 pm

How to specify secondary structure on downloaded I-TASSER?

Post by DavidB256 »

Hello! I am using I-TASSER downloaded onto my computer and could not figure out how to specify the secondary structure of specific residues in my input sequence, as can be done under "Option III" here: https://zhanglab.dcmb.med.umich.edu/I-TASSER/. Is there a command for including a text file that specifies secondary structures in locally-scheduled I-TASSER jobs? Thanks!
jlspzw
Posts: 31
Joined: Tue May 04, 2021 5:04 pm

Re: How to specify secondary structure on downloaded I-TASSER?

Post by jlspzw »

Hi DavidB256,

Unfortunately, the standalone version I-TASSER do not support self-defined secondary structure by commands. However you can modify by replace the seq.dat file in your data folder before doing I-TASSER simulation.

here is one example of seq.dat file

39 GLN 4 3
40 LYS 4 7
41 VAL 4 7
42 VAL 4 5
43 THR 1 1
44 LEU 1 4
45 THR 1 6
46 ASP 1 6
47 THR 1 7
48 THR 1 1
49 ASN 2 4
50 GLN 2 7
51 LYS 2 9
52 THR 2 9

the first column is residue index, the third column is secondary structure (SS) that used in I-TASSER, where

1 is coil (C), 2 is helix (H) and 4 is strand (E)

the last column is the confidence score of the SS state range from 1-9

when you run the runI-TASSER.pl, you can stop before the following line, ie add exit(1); before that line

printf "2.3 Predict solvent accessibility...\n";

then replace the seq.dat by yours

then remove the "exit(1);", re-run runI-TASSER.pl.

Let us know if you have any questions.

Thank you for using our software.

Best
IT team
DavidB256
Posts: 4
Joined: Fri Jun 11, 2021 4:01 pm

Re: How to specify secondary structure on downloaded I-TASSER?

Post by DavidB256 »

Thank you! Does 1 or 9 represent the highest degree of confidence in secondary structure?
jlspzw
Posts: 31
Joined: Tue May 04, 2021 5:04 pm

Re: How to specify secondary structure on downloaded I-TASSER?

Post by jlspzw »

9 is the highest
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