From owner-chemistry@ccl.net Wed Aug 20 13:41:00 2008 From: "Bernd Wendt bwendt]~[tripos.com" To: CCL Subject: CCL: Scaffolds for CoMFA contour plots Message-Id: <-37588-080820133935-17039-Nhfj0TOPKwmJ37usGVcJzQ##server.ccl.net> X-Original-From: "Bernd Wendt" Date: Wed, 20 Aug 2008 13:39:31 -0400 Sent to CCL by: "Bernd Wendt" [bwendt]*[tripos.com] Dear DD and Deepa, the Optimize QSAR only works with R-groups or sidechains, i.e. fragments with only one open valence. I guess by scaffolds you mean core structures with 2 or more variable R-groups attached. In this case Optimize QSAR would not be of any help. There are tables with such scaffolds to be found in the SYBYL tree, i.e. $TA_ROOT/demo/linux/sub2v.tbl or sub3v.tbl that you might want to try, but I would try another approach. Since you don't want to get too far away from the scaffolds of your training set, why don't you try the scaffold search option of the topomeric search tool in SYBYL. Given a scaffold-query, i.e any 2D-structure of a fragment with 2 or more open valences as input, you can search full-structure databases in like ACD or NCI or any other database you have available with 3D coordinates for suitable scaffold candidates for your CoMFA model. Best regards, Bernd bwendt[at]tripos.com Sent to CCL by: "Deepangi Pandit" [deepangi.pandit]*[gmail.com] Hi DD, I am not sure if you have tried this or looking for similar stuff but if you are using SYBYL there is an option for QSAR Optimization via option optimize QSAR. I do not remember the exact menu location but please search Tripos Bookshelf for QSAR optimization or optimize QSAR. I think there is also a tutorial about the same. Deepa On Mon, Aug 18, 2008 at 10:30 AM, D dean ddean86 _ gmail.com wrote: > > Sent to CCL by: "D dean" [ddean86*|*gmail.com] Hello, > > I had performed a 3D-QSAR analysis and got favorable electropositive (blue) and electronegative (red) contour maps. > > I am interested to know if there are a list of scaffolds which I can use for substituting near favorable electropositive and favorable electronegative contour regions. > > Most of the 3D-QSAR paper just say favorable regions, or just suggest carbonyl group near electronegative and free amino group near electropositive regions. > > If anyone can suggest a listing of such scaffolds which I can try it will be very heplpful to me and maybe also helpful to other beginners. > > Thank you for your time. > > Best regards, > > DD> > >