Hi Kirstie

It seems to me that you ask as if there was a given "native" conformation for this short molecule. In other words , do you want it fit to any target? If you have target and peptide, things would be different than if you just have the peptide and water.

Thank you for your reply Rafael Franco

We do know the native state of the peptide- it is disordered in water and adopts an alpha-helix in membrane-mimicking conditions in the presence of TFE from our CD work. We don't want to visualise the peptide bound to anything, just visualise the peptide in it's helical state. The goals we have are rather simplistic, but it seems the length of the peptide really limits the structural programme choices.

In terms of target, the peptide does share sequence homology with another peptide but it's rather low (50%) and if we're desperate I guess we can map it to that. Ideally, the native peptide would be the target (as we have modified the peptide and would like to observe the structural changes this has induced) and the modifications made would then be mapped on to this target.

I hope I've clarified things! Thanks again.

https://www.chemcomp.com/Products.htm

Dear Kirstie,

I am not sure whether it is what you’re looking for but did you try PEP-FOLD:

http://bioserv.rpbs.univ-paris-diderot.fr/services/PEP-FOLD/

http://bioserv.rpbs.univ-paris-diderot.fr/services/PEP-FOLD3/

Perhaps 24 AA might be too short but you could try I-Tasser:

https://zhanglab.ccmb.med.umich.edu/I-TASSER/

I have no personal experience with Avogadro but this seems promising to me as well:

https://avogadro.cc/docs/building-molecules/building-a-peptide/

PS. Perhaps out of topic but it seems to me that the tool MCPep might be interesting to check. This program predicts possible peptide-membrane configurations (and many more).

Anyway I hope this helps you any further.

Rob Keller thank you for your reply.

I have previously tried Pepfold, I've found it to be the least sophisticated of my limited options.

Currently running I-TASSER- it has allowed me in input a 24 aa sequence! It looks similar to Quark (created by the same group). I'm hoping it provides slightly more information than Quark, but it's difficult to tell until the server has analysed the structure.

Avogadro looks similar to pymol, which at least gives the option to highlight residues- a vast improvement on some of the modelling software I've previously been restricted to. Thank you so much for your help!

You can refer to below attached paper full-text, which has all the methodology detials and link to webservers.

Hi Kirstie, I think essentially what you are asking about is: "ab initio membrane protein/peptide structure prediction". The best tool I have used for such things is Rosetta. You need to locally install it, which is not necessarily straightforward. However, these are some links, and you could hunt around on their website for more information:

https://www.rosettacommons.org/docs/latest/release-notes

https://www.rosettacommons.org/manuals/archive/rosetta3.5_user_guide/db/d38/membrane_abinitio.html

You can use rosetta or pepfold3 both are good.