[ccp4bb]: searching for structural motifs

["Patrick J. Loll" <loll@pharm.med.upenn.edu>]

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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.

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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