Subject: Re: CCL:PDB 3D queries?

From: David Brown <[email-masked]>
Date: Mon, 27 Jul 1998 09:34:32 +0100

You should look at Iditis from Oxford Molecular, a comprehensive
database of derived information from the PDB.

To give just a flavor of the information available, the DISULPH table
contains:

Four letter Brookhaven PDB code
One letter model code
One letter polypeptide chain label for first Cys residue
Amino acid identifier of residue for first Cys residue
One letter polypeptide chain label for partner Cys residue
Amino acid identifier of residue for partner Cys residue
Bridge assignment responsibility
Extended Kabsch and Sander secondary structure assigment for first Cys
residue
Number of amino acid residues between two Cys residues
Extended Kabsch and Sander secondary structure assigment for partner Cys
residue
Inter C-alpha distance between two Cys residues
Inter C-beta distance between two Cys residues
Inter S-gamma distance between two Cys residues
Standard chi-1 torsion angle for first Cys residue
Standard chi-2 torsion angle for first Cys residue
Standard chi-3 torsion angle for first Cys residue
Standard chi-2 torsion angle for partner Cys residue
Standard chi-1 torsion angle for partner Cys residue
Incremental count of number of bridges in protein

> Hi,
> 
> What packages allow one to query the PDB in the same way one can query the
> Cambridge small-molecule database (eg. extract a histogram of NH...OC distances
> & angles, ring-ring distances & angles, atom-ring distances & angles, specified
> types of bond torsions and angles, etc.)?
> 
> I will summarize responses.  Thanks,
> 
> Bryan Marten, PhD
> Schering-Plough Pharmaceuticals
> [email-masked]

	David
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