From chemistry-request#* at *#server.ccl.net Mon Jul 8 15:37:05 2002 Received: from so.sd.lionbioscience.com ([209.68.255.43]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g68Jb4p31940 for ; Mon, 8 Jul 2002 15:37:04 -0400 Received: from tempest.sd.lionbioscience.com (tempest.sd.lionbioscience.com [10.8.0.8]) by so.sd.lionbioscience.com (8.11.3/8.11.3) with ESMTP id g68JZEg22215; Mon, 8 Jul 2002 12:35:23 -0700 (PDT) Received: by tempest.sd.lionbioscience.com with Internet Mail Service (5.5.2653.19) id ; Mon, 8 Jul 2002 12:35:01 -0700 Message-ID: From: Stephen Bowlus To: "'??'" Cc: "'dshobe:~at~:sud-chemieinc.com'" , "'chemistry&$at$&ccl.net'" Subject: RE: the most common structure Date: Mon, 8 Jul 2002 12:35:00 -0700 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C226B6.8C79EFA0" This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. ------_=_NextPart_001_01C226B6.8C79EFA0 Content-Type: text/plain; charset="gb2312" Content-Transfer-Encoding: quoted-printable 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=20 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. Cheers, Steve Bowlus > -----Original Message----- > From: chem_liqiang-!at!-sohu.com [mailto:chem_liqiang-!at!-sohu.com] > Sent: Sunday, July 07, 2002 11:00 AM > To: chemistry: at :ccl.net > Subject: CCL:the most common structure=20 >=20 >=20 > Sir/Miss=A3=BA > Good morning. > Who can tell me how to pick up the most common=20 > structure from a set of compounds, and save it into a=20 > structure file? Could you indicate to me further softwares=20 > able to perform the same task? I have SYBYL software, but no=20 > DISTILL module. >=20 > Thank you very much!=20 >=20 > Li Qiang >=20 > Shanghai Institute of Organic Chemistry > Chinese Academy of Sciences=20 >=20 > No.354 Road FengLin > ShangHai, 200032, China > Phone: 08621-64163300-2735 > Fax: 08621-64166128 >=20 ------_=_NextPart_001_01C226B6.8C79EFA0 Content-Type: text/html; charset="gb2312" Content-Transfer-Encoding: quoted-printable 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.

Cheers,
Steve Bowlus

> -----Original Message-----
> From: chem_liqiang(+ at +)sohu.com [mailto:chem_liqiang /at\sohu.com]<= /FONT>
> Sent: Sunday, July 07, 2002 11:00 AM
> To: chemistry ":at:" ccl.net
> Subject: CCL:the most common structure
>
>
> Sir/Miss=A3=BA
>     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
>

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