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How to specify secondary structure on downloaded I-TASSER?

Posted: Tue Jun 29, 2021 6:15 am
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!

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

Posted: Tue Jun 29, 2021 5:17 pm
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

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

Posted: Fri Jul 02, 2021 1:57 am
by DavidB256
Thank you! Does 1 or 9 represent the highest degree of confidence in secondary structure?

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

Posted: Sun Jul 04, 2021 11:28 pm
by jlspzw
9 is the highest