MedChem FAQ
Frequently asked questions about Daylight's HTML interface to MedChem database.
MedChem web-interface
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Current Medchem db
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MedChem web interface
Why is there a special interface for the MedChem database?
The HTML interface to MedChem is designed to make access as simple as
possible, implementing a "what do you want -- here it is" interface.
The end-user does not need to know about servers, database names, datatypes,
datatrees, thesaurus-orientation, ambiguous cross-references, etc.
The MedChem database contains a lot of information of interest to
pharmaceutical chemists. This interface is designed to deliver this
information quickly and reliably to users who do not need to be chemical
information specialists.
MedChem isn't unique in this respect: Daylight produces simplified interfaces
for other databases also.
What can I ask for?
You can specify any identifier in the database, specifically: SMILES, CAS
numbers, WLNs and all kinds of names. Except for SMILES and WLN, queries are
case-, whitespace-, and punctuation-insensitive.
Is this the same database distributed by Pomona College?
Sort of. This database started as the Medicinal Chemistry Project at Pomona
College. The MedChem Project became BioByte and the database followed.
This version is more comprehensive than previous versions.
Is this the same database distributed by BioByte?
Yes. Each version (e.g., "medchem00") is derived from data supplied by and
copyrighted by BioByte and is distributed under license with BioByte.
The Daylight version is reformatted slightly (Formula, CLOGP, CMR and
Conformation data are added).
Does the Daylight version contain all entries in the original?
Yes.
Is the complete MedChem database available online?
No. Our license with BioByte permits online distribution only for
demonstration purposes. Daylight can supply the complete MedChem database and
the software to deliver it from your own server. Hardware requirements are
minimal for the HTML interface (a UNIX workstation and 25-50 MB free disk
space).
Can I do substructure and similarity searching?
No. The current HTML interface is limited to looking up specific molecules.
How can I draw in a structure (rather than typing SMILES)?
Your choice of an editor depends on the kind of machine on which
you are working. This can be customized by editing the dcgi_env.sh
file.
The depictions are linked to the depict page. Why bother?
Clicking on any large depiction brings up the "Depict" (Interactive depiction
of SMILES) page. Editing the SMILES on this page changes the picture but does
not affect what data is shown when returning to MedChem.
Invoking the Depict page is simply a way of providing the SMILES
for any structure in a cut-and-paste-able form.
Why are "black-on-paper depictions" offered?
Depending on how your computer system is set up, color-on-black graphics may
not show up well when printed to monochromatic printers. The "black-on-paper"
option produces reasonably nice output with most browser/printer combinations.
It's not perfect (it's a GIF), but at least it's not transparent!
Can I save specific MedChem pages as a bookmarks?
Yes. You can save the initial "MedChem Database" page as a bookmark
to allow convenient access to this interface. Individual MedChem pages can be
added to your bookmark list: they will appear in the list named by database
and query string e.g., "medchem00: cisplatin". Such bookmarks are "live",
i.e., they reflect current database contents. Datatype selection is preserved
in bookmarks.
How can I view downloaded 3-D structures?
3-D data are downloaded as the MIME datatype "chemical/x-cex-3d".
WWW browsers such as Mosaic and Netscape allow you to
control how such data is dispatched. How this is done depends on your
operating system. For instance, on a Unix system, you need to add
"chemical/x-cex-3d" to the list of types in .mime.types and indicate
that you want the data dispatched to a 3D structure viewer (e.g.,
rasmol) in your .mailcap file.
Where can I get more information?
For general information about the MedChem database and Daylight's products,
click on the "Daylight Chemical Information Systems, Inc." link to the
right of the sunburst logo at the bottom of each page.
This should bring up Daylight's Home Page with lots of goodies.
For quotes, pricelists, demo tapes and other information not provided
in the Home Page, send e-mail to info@daylight.com.
For technical support, send e-mail to support@daylight.com.
Daylight Chemical Information Systems, Inc.
info@daylight.com