Re: [ccp4bb]: searching for structural motifs

[Kay Diederichs <kay.diederichs@uni-konstanz.de>]

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"Patrick J. Loll" wrote:
> 
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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.
> 
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
> 
> Patrick J. Loll, Ph. D.                             (215) 898-1294
> Department of Pharmacology                     FAX: (215) 573-2236
> University of Pennsylvania School of Medicine
> 3620 Hamilton Walk
> Philadelphia, PA  19104-6084  USA
> 
> loll@pharm.med.upenn.edu
> http://pharm.med.upenn.edu/Loll/loll_lab.html

I used Gerard Kleywegt's SPASM program for that purpose.
-- 
Kay Diederichs         http://strucbio.biologie.uni-konstanz.de/~kay 
email: Kay.Diederichs@uni-konstanz.de  Tel +49 7531 88 4049 Fax 3183
Fakultaet fuer Biologie, Universitaet Konstanz 
Box M656, D-78457 Konstanz, Germany