Re: [ccp4bb] Parseable residue-ligand and/or residue-nucleic acid interaction database?

2018-10-29 Thread John Berrisford 
Dear Lucas

You may want to look at credo
http://marid.bioc.cam.ac.uk/credo
We (PDBe) are working on integrating this into both our website and API. 

John
PDBe

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Lucas
Sent: 29 October 2018 13:53
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Parseable residue-ligand and/or residue-nucleic acid 
interaction database?

Just so that we don't reinvent the wheel: is there any database or webservice 
on which one can parse the list of residue-ligand interactions for the entire 
PDB? I'd like to programmatically obtain information such as "in PDB 3hdl the 
Calcium 306 is in contact with
Asp223 or in PDB 5gjb Arg388 is in contact with the phosphate in the nucleic 
acid chain B". I know this information is available through pdbsum via 
ligplot/nucplot, but I'm unaware if it is possible to download the entire 
interaction database and if it is parseable.



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[ccp4bb] Parseable residue-ligand and/or residue-nucleic acid interaction database?

2018-10-29 Thread Lucas 
Just so that we don't reinvent the wheel: is there any database or
webservice on which one can parse the list of residue-ligand
interactions for the entire PDB? I'd like to programmatically obtain
information such as "in PDB 3hdl the Calcium 306 is in contact with
Asp223 or in PDB 5gjb Arg388 is in contact with the phosphate in the
nucleic acid chain B". I know this information is available through
pdbsum via ligplot/nucplot, but I'm unaware if it is possible to
download the entire interaction database and if it is parseable.



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