MedChem FAQ

Frequently asked questions about Daylight's HTML interface to MedChem database.

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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 Daylight Chemical Information Systems, Inc.
info@daylight.com