[BioPython] protein-ligand interactions

[Peter Cock]

On Wed, Mar 18, 2009 at 9:05 AM, mitlox <mitlox at op.pl> wrote:
>
> Hello,
> I have a solved structure (1E8W) with a ligand and I would like to
> know which residues are within 3A of the ligand. This 3A is a cut
> off and should be using just for the C-alpha in each residue, but
> it would be great if I know which C-alpha belongs to a residue.
>
> I am newbie in Biopython/Python, maybe anyone know an
>  example how is it possible?

Hi,

I've got a couple of PDB examples on my personal website, and although
they need a little update to use NumPy instead of Numeric, I think the
page on doing protein contact maps would be very informative:
http://www.warwick.ac.uk/go/peter_cock/python/protein_contact_map/

In your case, for the protein in each residue you'll want to use just
the C-alpha atom (in the residue's atom dictionary under the key
"CA"), but I think you should loop over all the residues in the ligand
in order to find the least distance.

Peter