[RASMB] Regarding V-bar calculation of peptide containing non-natural amino acid

[prasun kumar]

Hi Mattia and the group:

Thank You for the response. I installed US-SOMO and just to check whether
it is working for peptides with non-natural amino acids, I used one PDB ID
(1GOE). It contains DPN and AIB.

Program says it has got unrecognised residues and asked me to take the
average value or stop processing......
I chose the first option and got the V-bar value.

Now the question is whether considering the average values for the
non-natural amino acids is a good idea or not.... If no then do you think I
should also go back and refer to the "bible".

I am doing my experiments in PBS+Water solvent (pH 7.4)

Regards
Prasun

PRASUN (ASHOKA)
Desire + stability = Resolution
Resolution + Hard work = Success

On Thu, Sep 28, 2017 at 10:49 AM, Rocco Mattia <mattia.rocco at hsanmartino.it>
wrote:

> Hello Prasun,
>
> if you have a PDB file for your peptide, you can try uploading it in
> US-SOMO and see if the non-standard AA are recognized and a vbar calculated.
>
> Otherwise, the computations are a bit complicated... we usually do them,
> when facing non-standard residues, using an Excel worksheet based on the
> "bible" for vbar calculations:  Durchschlag and Zipper, Prog. Colloid
> Polym. Sci. 94:20-39, 1994
>
> Hope this helps!
>
> Mattia
>
> ________________________________
>
> From: RASMB on behalf of prasun kumar
> Sent: Thu 9/28/2017 11:34 AM
> To: rasmb at list.rasmb.org
> Subject: [RASMB] Regarding V-bar calculation of peptide containing
> non-natural amino acid
>
>
> Hi All:
>
> I have a peptide that contain non-natural amino acids. My query: how to
> calculate the V-bar of this peptide?
> Any suggestions will be really helpful to me.
>
> Regards
> Prasun
>
> PRASUN (ASHOKA)
> Desire + stability = Resolution
> Resolution + Hard work = Success
>
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