Zhanglab forum

I wanted to ask you a question, as I have seen in the bibliography that
you have several programmes for modelling multidomain protein
structures. I am currently using M-SADA, as the DEMO programme does not
seem to be working at the moment.

I would like to ask you a question about the protein I am modelling, as
you are experts in this field. My protein currently has several domains,
two of which are mucin_I and mucin_II, which are very disordered and
Alphafold is unable to model them correctly. In this case, should I
ignore them? Is the M-SADA programme capable of modelling a structure
without taking these domains into account?

In addition, some of my domains have gaps because we have not been able
to determine a specific amino acid. Does this pose a problem for the
programme? Can they be removed and would that be sufficient?

Thank you very much in advance and congratulations on your work

Thank you for your message. We are working on restoring the servers on a new computational cluster and they should be restored as soon as possible. We apologize for any inconvenience.

For multidomain modelling, you may also consider D-I-TASSER or I-TASSER-MTD, both of which can be used to model multi-domain proteins. For the disordered mucin_I and mucin_II regions, you may try modelling them with these programs as well; if they remain unresolved, it is also reasonable to exclude them and focus on the structured domains. Small sequence gaps are usually not an issue, and removing the unresolved residues is typically sufficient.

Please feel free to reach out if you have any further questions, and thank you again for your interest in our work.

ZhangLab team