From owner-chemistry@ccl.net Sat Aug 9 11:49:01 2008 From: "Derek J. Cashman derek.cashman===gmail.com" To: CCL Subject: CCL: SAR predictions for this paticular question Message-Id: <-37528-080808185354-2641-4yVHu+cSPQDrW797eniqQw%x%server.ccl.net> X-Original-From: "Derek J. Cashman" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 8 Aug 2008 17:59:02 -0400 MIME-Version: 1.0 Sent to CCL by: "Derek J. Cashman" [derek.cashman%gmail.com] On Fri, Aug 8, 2008 at 4:12 PM, Nancy Ann Neale nealen!A!mail.nih.gov wrote: > > Sent to CCL by: "Nancy Ann Neale" [nealen#,#mail.nih.gov] > I am looking for recommendations for SAR softawre for a specific problem. > > What we have at this point is approximately 50 compounds that have bee qualitately analyzed for activity in a certain cell. We haven't structural data on the surface protein that shuttles substrates accross the membrane, but that is only the first step in detrmining what a good canddiate is. > > We have 'downstream' data on these compounds with respect to activity, IC50, and a selectivity ratio. > > My first thought is AutoDock, but am concerned that may not do the trick because of our lack of structural data of that protein. > > My goal is to train some program with the good amount of data we have to recognize adn ultimately predict reasonable candidates in the future for this application. > > Any suggestions are most welcome. Looks like this data set would be ideal for running a CoMFA study (Comparative Molecular Field Analysis) in SYBYL (www.tripos.com). Assuming that SYBYL is available or within your budget (it's a commercial package). Derek J. Cashman, Ph.D. derek.cashman+*+gmail.com "A Drug is any substance which, when injected into a rat, produces a publishable, scientific paper."