Number of known non-homologous protein struc's?

Sean Eddy eddy at wol.wustl.edu
Wed Aug 30 15:34:09 EST 1995


In article <41g3dd$rv3 at vixen.cso.uiuc.edu> c-gibas at ux4.cso.uiuc.edu (Cynthia Jeanne Gibas) writes:
  >If you're more concerned with fold types, check out the SCOP site, which is
  >an automated 'family tree' of all of the solved protein structures.  It's
  >based on the work of Murzin and Chothia, which paper I don't have in hand
  >at the moment.

Actually, the thing I really like about SCOP is that large parts of it
are the result of manual, expert classification by Alexei Murzin and
Cyrus Chothia. Many of the problems inherent in fully automated
classification schemes have been avoided. The partial automation
that's used is done to reduce the number of structures that Alexei has
to look at by eye -- detecting the obvious homologues, etc.

The SCOP reference is JMB 247:536-540, 1995. In the US, the SCOP mirror
site at PDB is http://www.pdb.bnl.gov/scop.

(Obligatory caveat: I'm biased; I'm a peripheral collaborator on the
SCOP project.)

A related database of protein folds from Janet Thornton's group is
CATH, at http://www.biochem.ucl.ac.uk/bsm/cath/CATHintro.html.

--
- Sean Eddy
- Dept. of Genetics, Washington University School of Medicine
- eddy at genetics.wustl.edu





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