Re: [ccp4bb]: searching for structural motifs

["Gerard \"DVD\" Kleywegt" <gerard@xray.bmc.uu.se>]

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> Not a CCP4 question, but:
> 
> 	How might one search the PDB for a structural motif?  E. g., given
> a particular motif (with an associated set of coordinates), how to find
> similar naturally occurring structures that can be superimposed onto my
> motif with an  rmsd better than some threshold?
> 
> 	Examples of what I mean by motif might be something like 3 helices
> arranged in a specific geometry, or a strand packed a particular way
> against a helix.

if the motif consists of a number of secondary structure
elements (SSEs) you can use dejavu (or other fold comparison
software such as dali, top and what have you); you can
use the dejavu web server at http://portray.bmc.uu.se/dejavu
or install the software locally (also requires access
to the pdb on a local disk; http://xray.bmc.uu.se/usf/dejavu.html)

if the motif is small (e.g., just two or three SSEs) or
not made up of SSEs at all (a strange loop, or a set of
ligand-binding residues for instance), you can use spasm
instead, again either through the web server (at url
http://portray.bmc.uu.se/spasm) or by installing the
software locally (http://xray.bmc.uu.se/usf/spasm.html)

--dvd

******************************************************************
                        Gerard J.  Kleywegt
Dept. of Cell & Molecular Biology  Bolshevik University of Uppsala
                Biomedical Centre  Box 596
                SE-751 24 Uppsala  SWEDEN

    http://xray.bmc.uu.se/gerard/  mailto:gerard@xray.bmc.uu.se
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