ECTOC-3 ConferenceSearching the conference molecular database

The search form

SMILES of the molecule:
For example (benzene): c1ccccc1

MDL MOLFILE or PDB file
If you cannot see a button next to the following box, then your browser may not work.
For Netscape users, select the file using the browse button. Entering text in the box will not work.

Submit the search query
If there has been a major mistake

Introduction

The conference molecular database has been setup for various reasons. Providing this facility will hopefully provide a value added component to this conference allowing the participants to search for molecules in the confernence. These molecules will allow the articles to be clustered so that they can improve the navigation around the conference.

We are using two THOR databases, one to store the article information such as the title etc. and the other stores the molecular information. A MERLIN server mirrors the molecular database allowing similarity searches to be performed. These databases were created using the Daylight toolkit. The similarity searches will take at least 20 seconds to perform, but the network traffic may make the search appear longer. Molecules added by the authors will be available within an hour when the MERLIN database is refreshed.

How to perform a search

There are three ways of creating a molecular search query: SMILES, reaction or molecule drawn in ISIS draw or using x-ray crystallographic data.

  1. SMILES: These can be typed straight into the form below. Instructions on how to create a SMILES by 'hand' can be found at the SMILES home page at Daylight Chemical Information Systems, Inc. or locally on the conference server.

    It is possible to use Chemdraw Pro (has been tested with version 3.5) to create SMILES. Firstly draw the molecule on the page. Select the molecule using the select tool. In the menus you will find Edit->Copy as->SMILES. Select this and the SMILES will appear on the clipboard. Go back to your web browser and paste the SMILES in to the SMILES box in the form.

  2. Using ISIS draw: This will only work for Netscape 2.x and above and browsers that support file uploading to the conference server. Draw your query molecule in ISIS draw. Select the molecule using the select tool. In the menus select File->Export->Molfile... and save the molecule on your hard disk. Return to your browser and select the 'Browse...' button in the form and find and select your MOLfile in the dialogue box. You may need to change the 'Files of type:' at the bottom to 'All Files (*.*)' or 'MDL MOLFile (*.mol)' to see the MOLFiles. Click on 'Open' to add it to the form.

  3. X-ray crystallographic data (PDB files): This will only work for Netscape 2.x and above and browsers that support file uploading to the conference server. The PDB file will need to be on your hard disk. In your browser select the 'Browse...' button in the form and find and select your PDB file in the dialogue box. You may need to change the 'Files of type:' at the bottom to 'All Files (*.*)' or 'Brookhaven Protein Databank (*.pdb)' to see the molecule files. Click on 'Open' to add it to the form.

    Once the molecular query is in the form, press the 'Search for similar molecules' button. You can supply both a SMILES and a molecule in MOLFile or PDB file formats, but you must make sure that they represent the same molecule!

    Notes to authors

    We are encouraging authors to submit molecules from their articles to the conference molecular database. Please go to the molecule registration form. You will need your conference ID and password.

    Chris Leach 10/04/997