Software To Introduce Ss Bonds

Question

[Elmo]

Dear experts,

I want to introduce SS bonds to my protein models modelled by Modeller and I-tasser. What bioinformatics tool allows me to introduce them? And how can I check the energy after introducing the SS bonds?

Thanking you in advance.

Answer 1

[Pappu]

There is an option in modeller to add SS bonds.

[Elmo]

Hi Pappu, thanks for replying. I used Pymol instead. :)

Answer 2

[João Rodrigues]

SS bonds are determined by distance mainly. In PyMOL you can 'see' them only if the two S atoms are within a specific cutoff.

In MODELLER you can force a particular pair of atoms to be involved in a SS bond using special restraints. But usually, if these are conserved in the template, they are detected by the software automatically and included in the modelling. I-Tasser works the same, allowing you to input a specific atom-atom distance.