CCL: Scaffolds for CoMFA contour plots

 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
 <owner-chemistry#%#ccl.net> 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>
 >
 >