ChemMart

TJ O'Donnell
Tom Doman
G.D. Searle, Skokie, IL

ChemMart is a web application that uses the ChemDraw web plug-in to allow users to input molecular structures. It takes the SMILES string output by ChemDraw and passes it on to one of several web-server cgi scripts for further processing. The available functions are:

• Find: to find the exact structure.
• SubStructure: to find structures containing the structure.
• Neighbor: to find the nearest neighbors of the structure.
• SMARTS: to do a SMARTS search. User may modify the SMARTS string of the structure by hand.
• clogP: to compute the logP of the stucture.
• Ruleof5: to compute Lipinski's rules for the structure.
• 3DStructure: to generate Concord 3D coordinates for the structure.
• SurfaceArea: to compute total and polar surface area of Concord-generated structure.
• Lookup: to look up the name of a compound; does not require structure, but returns structure to ChemDraw.

Lookup and structural searches (Find, SubStructure, Neighbor and SMARTS) are accomplished using the Daylight Thor database system and the Merlin/mcl program. There are several databases available at Searle, including the ACD database as well as Thor databases of Searle proprietary compounds. With minor modifications, it is possible to interface ChemMart to any Thor database.

A sample page shows the ChemDraw plugin and available application buttons. This page has a working ChemDraw plug-in, provided you have the plug-in properly installed on your machine. The application buttons do not work as they would if a real web-server with databases and Daylight software were involved. Instead, pushing the Find button for example, will show you a sample output page generated from a previous search of ACD.

Many of the application buttons have an options button associated with them. The options button allows the user to modify certain aspects of function, such as which databases to search and which parameters to use for a neighbor search. The actual options buttons on the sample page will not function, since this is just a sample. You can view a sample options page to get a sense of the available options for a neighbor search.

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