Discussion group for the ARIA software

[Benjamin Bardiaux <bardiaux AT pasteur.fr>]

Hi,

ARIA provides (undocumented) support for isopeptide bonds between side-chains 
of Asp/Asn and Lys residues.
In the GUI,, "Add... > Isopeptide bonds" and specify the 2 involved residues.

Please make sure you have the latest version installed
http://aria.pasteur.fr/archives/aria2.3.2.tar.gz

In case your bridge is between other residues types (Glu ?), you can easily modify the ISOP patch in 
aria2.3/cns/toppar/topallhdg5.3.pro

(used in this paper for example 
https://pubs.rsc.org/en/content/articlelanding/2016/OB/C6OB01745B)

Best,

Benjamin

On 07/09/2022 14:49, c.williams AT bristol.ac.uk wrote:
> Hello,
>
> We are looking to calculate the structures of a family of peptides constrained
> with a lactam bridge ideally using ARIA. Does anyone now how to go about
> modifying ARIA and CNS to handle the lactam side-chain?
>
> Best wishes


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Dr Benjamin Bardiaux      bardiaux AT pasteur.fr
Unité de Bioinformatique Structurale
CNRS UMR3528 - Institut Pasteur
25,28 rue du Docteur Roux 75015 Paris, France
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