Sequence Searches for Structural Info

[POSTMASTER at NBRF.GEORGETOWN.EDU]

In message <9210280041.AA23415 at net.bio.net> David Lapointe, 
lapointe at uthscsa.edu, asked

> is there a way to make a sequence 
> comparison (protein) against sequences from a structural database, NRL_3D 
> for example.

Yes.  On October 1 we announced that we had added the ability to conduct
FASTA searches against the NRL_3D database only, as opposed to the normal
suite of PIR1 + PIR2 + PIR3 + NRL_3D + PATCHX.  Here is the full text of
that announcement.

| 5. FASTA Searches for NRL_3D Only
| 
| Some users had suggested that they wanted to do FASTA sequence searches
| only for the sequences with known 3-dimensional structures, the sequences
| extracted from the Brookhaven Protein Data Bank in NRL_3D.  Normally our
| FASTA searches are done against all the protein databases, PIR1, PIR2, PIR3,
| the non-redundant PATCHX (described in the August announcement and in part 2
| above) and NRL_3D.  Now when the command
|   USE BASES NRL_3D
| is used before a SEARCH command, only the NRL_3D database will be used for
| the FASTA search.  Otherwise, all the protein databases will be used.
| 
| Thanks to Ada Prochnicka-Chalufour at the Pasteur Institute for her helpful
| suggestion and her hospitality this spring.

------------------------------------------------------------------------
                                 Dr. John S. Garavelli
                                 Database Coordinator
                                 Protein Information Resource
                                 National Biomedical Research Foundation
                                 Washington, DC  20007
                                 POSTMASTER at GUNBRF.BITNET
                                 POSTMASTER at NBRF.Georgetown.Edu