RE: the most common structure

Title: RE: the most common structure

Since you refer to the Distill module, I infer you are looking for the "Maximal Common Substructure" (in Tripos parlance).  This will entail a lot of trying this and trying that, but one way to attack the problem is

0) Just to make visualization easier, delete all H > from the compounds in your database.
1) select a "representative" molecule from the database.
2) guess the largest substructure, and delete all other atoms
  - You can make a guess and run, or you can nibble away at the molecule by deleting "trivial" functionality
3) run File > Align Database using the structure > from 2 as the alignment template
  - If the fragment is present in every molecule, the alignment will run without any messages informing you that the structure is not present.

4) iterate steps 2 and 3 until the alignment step gives no messages.  You can check by loading the database into Sybyl (database get * m2 retrieve); the aligned molecules will stack up very clearly using the substructure from 2

This does not guarantee that the fragment you find is the largest or only large common fragment, but you can try other starting points as well.

Steve Bowlus

> -----Original Message-----
> From: chem_liqiang %-% at %-% [mailto:chem_liqiang %-% at %-%]
> Sent: Sunday, July 07, 2002 11:00 AM
> To: chemistry %-% at %-%
> Subject: CCL:the most common structure
> Sir/Miss:
>     Good morning.
>       Who can tell me how to pick up the most common
> structure from a set of compounds, and save it into a
> structure file? Could you indicate to me further softwares
> able to perform the same task? I have SYBYL software, but no
> DISTILL module.
>       Thank you very much!
> Li Qiang
> Shanghai Institute of Organic Chemistry
> Chinese Academy of Sciences
> No.354 Road FengLin
> ShangHai, 200032, China
> Phone: 08621-64163300-2735
> Fax: 08621-64166128