hi andy,
we have recently applied this server
http://211.25.251.163/assam/imaaagine/
Nadzirin,N.,Willett,P.,Artymiuk,P. J.&Firdaus-Raih,M.IMAAAGINE: a
webserver for searching hypothetical 3D amino acid side chain
arrangements in the Protein Data Bank.Nucleic Acids Res.41,W432–440(2013)
to find a similar arrangement of histidine residues in contact with a
serine and a hydrophobic residue
figure 4A in
https://www.biorxiv.org/content/10.1101/2021.02.05.429362v1.full
hth,
tim
On 2022-11-23 11:16, Andrew Lovering wrote:
Dear CCP4 list,
I have just tried accessing the “old” EBI PDBeMotif link and it is
non-functional. Assuming that it may or may not be moved/unavailable,
I am asking what your favourite methods are for mapping similar
residue interactions in dissimilar folds
i.e. if you have a nice network of 3 residues on “your” fold, what are
the ways in which you can then find a similar arrangement on others?
Thanks!
Andy
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