[BiO BB] protein families

[Iddo Friedberg]

Depends on what you mean by "family"

CATH and SCOP assign proteins in a hierarchical manner to classes, folds,
superfamilies, families based on sequence based (SCOP) and structure based
(CATH) similarities. Both are manually or semi-manually curated. FSSP does
the same task automatically. All three are in a high rate of agreement
(75-80%) regarding their calssifications. Of course, you are limited to
the proteins in PDB only: the ones for which there are solved structures.

If you wish to consider more sequecnes, then other assignemetns are
possible, depending on your purpose. Pfam is a good example.

I suggest you get a good bioinformatics textbook, such as David Mount's,
or Baxevantis, and look through the different classification schemes, and
choose the one which suits your purpose best.

./I

--
Iddo Friedberg, Ph.D.
The Burnham Institute
10901 N. Torrey Pines Rd.
La Jolla, CA 92037, USA
Tel: +1 (858) 646 3100 x3516
Fax: +1 (858) 646 3171
http://ffas.ljcrf.edu/~iddo

On Fri, 26 Sep 2003, Liu Haifeng wrote:

> Hi,
> 
> I am trying to find a collection of protein sequences  which have been
> correctly assigned to different families.   Anybody can suggest where to
> obtain such kind of data?  PDB and Swiss-Prot seem to provide sequences but
> without family information.
> 
> Would appreciate your help, thanks a lot!
> 
> Sincerely
> 
> Haifeng Liu
> 
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