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RE: Ligand search in PDB

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Hi Derek,

> Does anyone know of a good program which could take the coordinates of a
> ligand (in my case ATP) and run a search of the PDB to find the most similar
> conformations out of all the complexes present? Or one which at least tries
> to extract the coordinates and superimpose them on the search set? There are
> 53 structures with ATP in the PDB and to do the analysis by hand is rather
> laborious!

We have used Gerard Kleywegt's SPASM with great success in the search for
similar metal-binding sites. I don't know how this program would react to a
non-protein moiety, but I don't think it should pose any problems. Just supply
the coordinates of your ATP to the program and it'll conduct a search of the
entire data base.
But please consult http://alpha2.bmc.uu.se/~gerard/usf/spasm.html or J. Mol.
Biol. (1999), 285, 1887-1897 for more information.

Good searching...


     /_/\       Ditlev E. Brodersen       Phone: +45 8942 5021
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