a problem with the modeling from I-Tasser webserver

[himada97]

Hi,
I have submitted a peptide of 13 amino acids to be modelled using I-TASSER with a bond restraint between the two S atoms because the peptide is cyclic.
However, the results contained strange bonds, and one side chain was not attached to the backbone atoms and the two S atoms are away from each other.

This is the link of the results: https://zhanggroup.org/I-TASSER/output/S811836/

How can i solve this problem?

[XiZhang]

Dear user,

Thank you for using I-TASSER. At present, I-TASSER is tailored to model linear protein structures; unfortunately, it does not support cyclic peptides.

Best,
Xi

[himada97]

Thank you for your reply.
By cyclic peptides i dont mean that the amide group of the first amino acid is attached to the carboxylic group of the last amino acid. The peptide i want to model just has a disulfide bond between the first and last amino acid (sequence: CTVALPGGYVRVC) but the terminals are not attached to each other.

[ava951robinson]

Hello,
Group of the first amino acid is attached to the carboxylic group of the last amino acid. The peptide i want to model just has a disulfide bond between the first and last amino acid (sequence: CTVALPGGYVRVC) but the terminals are not attached to each other.

[JosepRoney]

Hi,
I have submitted a peptide of 13 amino acids to be modelled using I-TASSER with a bond restraint between the two S atoms because the peptide is cyclic.
However, the results contained strange bonds, and one side chain was not attached to the backbone atoms and the two S atoms are away from each other.

This is the link of the results: https://zhanggroup.org/I-TASSER/output/S811836/msn games

How can i solve this problem?

Go on! Even with bond restraints, it doesn’t establish a real covalent linkage between two residues unless it’s interpreted correctly.