proteins motifs databases

Gribskov, Michael gribskov at FCRFV1.NCIFCRF.GOV
Thu Aug 23 10:18:00 EST 1990


Sorry for the delayed reply, I assumed that there would be much more 
traffic on this question.  There are several projects underway to gather 
libraries, dictionaries, or databases of proteins structureal and/or sequence 
motifs.  My apologies in advance if I have misrepresented any of the 
material below -- obviously you should contact the origianl authors for 
details.  Some of the projects I know of are:

Randy Smith
Molecular Biology Computer Research Resource
RSMITH @ MBCRR.HARVARD.EDU
I think these patterns derive from alignment and clustering of all 
protein sequences in the protein database.  They are regular expressions
somewhat like the PROSITE patterns.  Available by ftp, and from EMBL and
U.Houston list servers (name PLSEARCH)
Ref: Smith and Smith (1990) PNAS 87,118-122.

John Wooton
National Center for Biotechnology Information
WOOTON @ NCBI.NLM.NIH.GOV
Patterns derived from both structure and sequence.  About 150 patterns, I think.
I'm not sure of the availability.

Michael Gribskov (Myself)
National Cancer Institute
GRIBSKOV @ NCIFCRF.GOV
Scoring matrices including position specific gap weights (Profiles)
which have been proven to detect sequence and structural patterns 
in a statistically significant way.  Currently about 30 profiles, mostly
of patterns of supersecondary structure, domains, and sequence motifs.
In the near future the corresponding alignments will also be available.
Publically available by E-mail and tape.
Ref: Gribskov et al., (1990) Met. Enzymol. 183,146-159.


Michael Gribskov
NCI - FCRDC
GRIBSKOV @ NCIFCRF.GOV
(301) 846-5031





More information about the Proteins mailing list