The BioMolecular Engineering Research Center & Molecular Biology
Computer Research Resource at Boston University (collectively
referred to here as BMERC) announces the availability of its Gopher
and World Wide Web (WWW) servers.
* The URL for the BMERC WWW server Home Page is:
http://bmerc-www.bu.edu/
* The gopher server can be accessed at the address given immediately
below. NOTE that the gopher can be accessed BOTH through gopher
and through a link provided on the BMERC WWW server Home Page.
bmerc-gopher.bu.edu
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The BMERC research objectives are summarized immediately below, and the
tools and interfaces described below which are available through the BMERC
gopher/WWW servers either support, or result from, the Center's work.
* To develop statistical and other computational approaches
which will detect syntactic and semantic patterns in DNA,
RNA, and protein sequences.
* To use statistical/computational approaches to identify the
structure, function, and regulation associated with such
patterns.
The component tools and interfaces, described below, are in an early stage of
development. We will continue to expand and develop these tools/interfaces
based on our own experiences with them, and by actively soliciting and
incorporating feedback from our collaborators, user community, and beta
test sites.
E-MAIL SERVER
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An e-mail server, called the Protein Sequence Analysis (PSA) System,
is available for researchers who have amino acid sequences for
proteins of unknown structure and for which no homologous
sequences are known. The server takes a single amino acid sequence
as input, and analyzes it to determine the probable tertiary
structural class of the protein and the probable secondary
structure for each of the residues. The output consists of four
files which are emailed to the requestor; three postscript files
which graphically summarize the analysis, and a text file.
Instructions for accessing the server, a short description of the
calculations being performed and associated journal references are
available through the gopher/WWW servers.
PROTEIN STRUCTURE/HOMOLOG DATABASE
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The gopher/WWW servers provide access to ProLink, a locally-developed
integrated database of protein structure, sequence homolog, and
functional pattern information installed in a relational format under
Sybase.
The current data is derived from the Brookhaven Protein Data
Bank (proteins of known structure), Protein Family Pattern Database
(also known as the Plsearch Database), Enzyme Nomenclature Database,
Protein Core Structures Database (currently under development here at
BMERC), and includes homolog links to the BLOCKS database, GenPept,
SWISS-PROT and Medline. It also has indirect links to Prosite, OMIM
and GDB databases.
Currently, ProLink can be searched using either the gopher/WWW SQL query
library, a set of prepackaged SQL queries, or an experimental mosaic-
based forms interface. PDB IDs in the forms-based search output
are hotlinked to the 'Molecules R Us' facility at NIH. This
facility permits the user to specify a variety of formats in which
the molecular data can be presented, including a format suitable for
interactive display, this latter format requiring that the client has
a suitable viewer such as RasMol installed. In the near future, access
to ProLink will be greatly expanded by increasing the size of the SQL
query library, and by implementing additional forms.
SOFTWARE DISTRIBUTION
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Through its FTP site, accessible through its gopher/WWW servers, BMERC
distributes, free of charge as part of its dissemination program, software
that it develops in meeting the objectives listed above, as well as
non-commerical software developed by others, datafiles, and support
information. In particular, the PLSearch database of homologous protein family
patterns, and the associated search-and-discovery software, is
available.
Bill Schmidt
Interface Specialist
BioMolecular Engineering Research Center (BMERC)
Boston University
36 Cummington Street
Boston, MA 02215 USA
(617) 353-7123
gophradm at darwin.bu.eduwwwadmin at darwin.bu.edu
