[BiO BB] protein families
idoerg at burnham.org
Fri Sep 26 02:51:18 EDT 2003
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.
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
On Fri, 26 Sep 2003, Liu Haifeng wrote:
> 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!
> Haifeng Liu
> BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org
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