From owner-chemistry@ccl.net Fri Mar 24 20:02:01 2006 From: "Dominic Ryan dominic.ryan,,comcast.net" To: CCL Subject: CCL: how to choose the bioactive conformation for CoMFA? Message-Id: <-31323-060324193610-32718-hiR/g/PxkWBPXW6a1qx+Gg:server.ccl.net> X-Original-From: "Dominic Ryan" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 24 Mar 2006 18:57:49 -0500 MIME-Version: 1.0 Sent to CCL by: "Dominic Ryan" [dominic.ryan _ comcast.net] It is important to realize that there are usually a reasonably large number of low energy conformations and that picking the lowest is no assurance that you have picked the relevant one. In addition, one has to worry about lowest *free* energy, and in the right environment, not simple mechanics minimization. Dominic Ryan -----Original Message----- > From: owner-chemistry-x-ccl.net [mailto:owner-chemistry-x-ccl.net] Sent: Friday, March 24, 2006 5:55 PM To: Ryan, M Dominic Subject: CCL: how to choose the bioactive conformation for CoMFA? Sent to CCL by: "Pankaj Daga" [pdaga+*+olemiss.edu] IN many cases, if the bioactive conformation is not available, the minimum energy conformation is considered to be the bioactive conformation. Minimum energy conformation can be obtained by conformational search of the molecule. Cheers panda > Sent to CCL by: "Shobe, David" [dshobe||sud-chemieinc.com] > C Sakthivel wrote: > > How do I choose the bioactive conformation of a > > perticular compound if such type of compounds were not > investigated earlier? > > I'd be surprised if there were a general method for > this...it all depends on which proteins it's supposed to > interact with (the bioactive conformation would be > whichever conformation fits the protein better), and it > doesn't sound like you have that information. > > > --David Shobe, Ph.D., M.L.S. > Süd-Chemie, Inc. > phone (502) 634-7409 > fax (502) 634-7724 > > Don't bother flaming me: I'm behind a firewall. > > > > > > -----Original Message----- > > From: owner-chemistry()ccl.net > [mailto:owner-chemistry()ccl.net] Sent: Wednesday, March > 22, 2006 6:48 PM To: Shobe, David > Subject: CCL: how to choose the bioactive conformation for > CoMFA? > > Sent to CCL by: Sakthivel C [skvchem[]yahoo.com] > --0-882663183-1143036218=:29550 Content-Type: text/plain; > charset=iso-8859-1 Content-Transfer-Encoding: 8bit > > Dear CCLers, > I'm working on 3D QSAR studies of some ancancer drugs > that are developed in our lab. Former members of our > group synthesized & studied the ancancer activity for > those compounds. I want to use the activity data for my > 3D QSAR studies (CoMFA & CoMSIA) and identify some new > compounds in same series. I learnt that choosing a wrong > bioactive conformer would lead to worng results. > So, my question is > How do I choose the bioactive conformation of a > perticular compound if such type of compounds were not > investigated earlier? > > Can any one suggest me? > > Looking forward to hear from you. > > Sincerely, > > C Sakthivel > Bharathidasan University > India > > > C. SAKTHIVEL > Research Scholar > School of Chemistry > Bharathidsan University > Tiruchirappalli 620 024 > TN, India > E-mail: skvchem~!~yahoo.com > skv_chem~!~yahoo.co.in > > > > > --------------------------------- > Yahoo! Mail > Use Photomail to share photos without annoying > attachments. --0-882663183-1143036218=:29550 > Content-Type: text/html; charset=iso-8859-1 > Content-Transfer-Encoding: 8bit > >
Dear CCLers,
I'm working on 3D QSAR > studies of some ancancer drugs that are developed in our > lab. Former members of our group synthesized & > studied the ancancer activity for those compounds. I > want to use the activity data for my 3D QSAR studies > (CoMFA & CoMSIA) and identify some new compounds > in same series. I learnt that choosing a wrong > bioactive conformer would lead to worng results. >
So, my question is
How > do I choose the bioactive conformation of a perticular > compound if such type of compounds were not > investigated earlier?
>
Can any one suggest me?
>
Looking forward to hear from you.
> ;
Sincerely,
C > Sakthivel
Bharathidasan University
>
India


color=#00007f>C. SAKTHIVEL FONT>
Research > Scholar
color=#ff007f>School of Chemistry
face=arial color=#ff007f>Bharathidsan > University
color=#ff007f>Tiruchirappalli 620 024
>
TN, India
> >

>

Yahoo! Mail
> href="http://pa.yahoo.com/*http://us.rd.yahoo.com/evt=3886 > 7/*http://photomail.mail.yahoo.com">Use Photomail to > share photos without annoying attachments. > --0-882663183-1143036218=:29550--http://www.ccl.net/cgi-bi > n/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_uns > ub.shtmlhttp://www.ccl.net/spammers.txtThis e-mail message > may contain confidential and / or privileged information. > If you are not an addressee or otherwise authorized to > receive this message, you should not use, copy, disclose > or take any action based on this e-mail or any information > contained in the message. If you have received this > material in error, please advise the sender immediately by > reply e-mail and delete this message. Thank you. > > > > -= This is automatically added to each message by the > mailing script =- To recover the email address of the > author of the message, please change the strange > characters on the top line to the _._ sign. You can also> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, > Password: search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > -+-+-+-+-+-+-+ > > > > Pankaj R. Daga Department of Medicinal Chemistry School of Pharmacy 417 Faser Hall University of Mississippi University, MS, 38677-1848 USAhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt