CCL: how to choose the bioactive conformation for CoMFA?



 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
 >
 > <div>Dear CCLers,</div>  <div>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.
 > </div>  <div>So, my question is </div>
 <div><STRONG>How
 > do I choose the bioactive conformation of a perticular
 > compound if such type of compounds were not
 > investigated earlier?</STRONG></div>  <div> </div>
 > <div>Can any one suggest me?</div>  <div> </div>
 > <div>Looking forward to hear from you.</div>  <div>
 > ;</div>  <div>Sincerely,</div>  <div> </div>
 <div>C
 > Sakthivel</div>  <div>Bharathidasan University</div>
 > <div>India</div><BR>
 <BR>
 <DIV> <DIV> <DIV><FONT face=arial
 > color=#00007f><STRONG>C. SAKTHIVEL</STRONG></!
 >  FONT></DIV> <DIV><FONT face=arial
 color=#ff007f>Research
 > Scholar</FONT></DIV> <DIV><FONT face=arial
 > color=#ff007f>School of Chemistry</FONT></DIV>
 <DIV><FONT
 > face=arial color=#ff007f>Bharathidsan
 > University</FONT></DIV> <DIV><FONT face=arial
 > color=#ff007f>Tiruchirappalli 620 024</FONT></DIV>
 > <DIV><FONT face=arial color=#ff007f>TN,
 India</FONT></DIV>
 > <DIV><FONT color=#00007f><FONT face=arial>E-mail:
 > </FONT><A href="mailto:skvchem~!~yahoo.com";><FONT
 >
 face=arial>skvchem~!~yahoo.com</FONT></A></FONT></DIV>
 > <DIV><FONT color=#00007f><FONT face=arial>
 > ;
 > </FONT><A href="mailto:skv_chem~!~yahoo.co.in";><FONT
 > face=arial>skv_chem~!~yahoo.co.in</FONT></A><FONT
 > face=arial>
 </FONT></FONT></DIV></DIV></DIV><p>
 >         <hr size=1> Yahoo! Mail<br>
 > <a
 >
 href="http://pa.yahoo.com/*http://us.rd.yahoo.com/evt=3886
 > 7/*http://photomail.mail.yahoo.com">Use
 Photomail</a> to
 > share photos without annoying attachments.
 >
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 Pankaj R. Daga
 Department of Medicinal Chemistry
 School of Pharmacy
 417 Faser Hall
 University of Mississippi
 University, MS, 38677-1848
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