[ccp4bb] PISA and ligands with non-natural amino acids

[Herman . Schreuder]

Dear Bulletin board,

I am looking at protein complexes with ligands containing non-natural amino 
acids. When I run PISA, I get the total area of the ligand, as well as the area 
of the ligand-protein interface, but hydrogen bonds and salt links are not 
recognized. I therefore do not think the calculated DeltaG values can be 
trusted. Is there a way to specify non-natural ligands for PISA, or does it 
only work for amino acids which have been calibrated with help of a large 
number pdb structures?

Thank you for your help!
Herman

Re: [ccp4bb] PISA and ligands with non-natural amino acids

[Eugene Krissinel]

Dear Herman,

I am looking at protein complexes with ligands containing non-natural amino 
acids. When I run PISA, I get the total area of the ligand, as well as the area 
of the ligand-protein interface, but hydrogen bonds and salt links are not 
recognized. I therefore do not think the calculated DeltaG values can be 
trusted. Is there a way to specify non-natural ligands for PISA, or does it 
only work for amino acids which have been calibrated with help of a large 
number pdb structures?

- this is exactly the case at the moment.

Eugene



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