ECTOC-3 ConferenceRegistering molecules to the conference database

The registration form

SMILES of the molecule
For example (benzene): c1ccccc1

Upload 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.

ACD Structure Drawing Applet
You would see ACD Structure Drawing Applet here if your browser were able to work with Java applets. If you are user of Netscape Navigator 3.0 for Windows 3.1 that does not work with Java applets, please visit Netscape's Web site to download Navigator 3.01 for Windows 3.1 that does work with Java applets.

Advanced Chemistry Development, Inc.
Reference
Enter the molecule's reference or Scheme number so that this can be referenced back to your article.
For example:10a, Figure 16, or Scheme 2

Submit the molecule
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 registration will take at least 30 seconds to perform, but the network traffic may make the submission appear longer. Molecules added will be available within an hour when the MERLIN database is refreshed.

How to register a molecule

There are three ways of registering a molecule: 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. If you use other programs to generate your MOLfile please make sure that the end of the file has M[space][space]END at the end of the file. Otherwise the submission will never finish.

  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. Make sure that there are CONECT records in the file. The database server generates SMILES strings from this information.

  4. ACD Drawing Applet: What ever is drawn in the applet will become the search query. You will need a Java capable browser for this. The full instructions to use this applet are at ACDLabs.

    Once the molecule is in the form, press the 'Register the molecule to the conference' 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!

    These instructions have been aimed at creating new moelcules. Most authors will have already done most of the hard work when they created the artwork for their article. These instructions apply but instead of drawing the molecule, load the reaction scheme. Make sure that any abreviations are expanded to their molecular equiverlent, or otherwise the abreviation is usually reduced down to a lonely methyl group! We can accept reactions, just make sure that the reaction arrow are not included as they become carbon chains!

    Chris Leach 10/04/1997