ECHET98 ConferenceRegistering molecules to the database

EITHER Define a molecule using SMILES: (For example benzene is c1ccccc1 )
OR Define a molecule using a locally saved MDL MOLFILE or PDB file. Select the file using the browse button. Entering text in the box will not work. If you cannot see a button next to the following box, then upgrade your browser to Netscape 3 or 4 or IE 4.
Enter a reference or Scheme number to reference back to your article. For example:10a, Figure 16, or Scheme 2
once a SMILES string or file have been entered. This might take 30+ seconds.
if there has been a major mistake.

Help on registering a molecule

There are two ways of creating a molecular entry.
  1. SMILES strings: This is an atom-connection descriptor which can be generated, typed or pasted straight into the box above. To generate a SMILES string, use one of the following methods;
  2. Using a locally saved molecule or PDB file: This will only work for Netscape 2.x and above and browsers that support file uploading to the conference server. Generate a Molfile using ISIS draw or ChemDraw. 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 string M[space][space]END is at the end of the file, otherwise the submission will fail. Follow a similar procedure for 'Brookhaven Protein Databank (*.pdb)'. Make sure that there are CONECT records in the file. The database server generates SMILES strings from this information. Most good modelling programs will generate such records. Crystallographic coordinates should be first converted from e.g. SHELX form to MDL molfile or PDB format.

    Once the molecule is in the form, press the 'submit the molecule' button. 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.

    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 equivalent (i.e. do not use R1 etc but expand it out fully) or otherwise the abreviation is usually converted to a lonely methyl group! We can accept reactions, just make sure that the reaction arrows are not included as they become carbon chains!

    Searching for molecules

    To see what others have submitted, please go to the form.


    The conference molecular database has been setup to allow participants to search for molecules described within articles and posters, and to allow molecular fingerprinting of each article on the basis of molecular similarity.

    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.

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