Subject: CCL: two questions about CoMFA

From: Jinsong Zhao <zh_jinsong{at}yahoo.com.cn>
Date: Thu, 22 Apr 2004 23:15:54 +0800 (CST)

Dear all,

I have two questions about CoMFA when I use SYBYL 6.7 package.

The first one is about View CoMFA. In general, the CoMFA
results is displayed with the contour map. In the View CoMFA
dialog, the default value for favored field is set to 80%,
and for unfavored field is set to 20% in the contour
specifications. Why those value not set to 100%, for we
could see all the favored and unfavored filed around the
molecule. What's the meaning for those value, and is it
necessary to change them?

The other question is about "Column Filtering" in PLS. I
find the different column filtering could result in
different contribution of two field to biological activity,
and there is no consistency. In "Ligand-Based Design Manual:
QSAR", it said "If you inadvertently left column filtering
OFF, the relative electrostatic and steric contributions
will be about 73% and 26%, respectively. For most work, it
is better to leave filtering OFF for uncrossvalidated
analyses. For the purpose of this tutorial, however, the
gain in speed offsets the loss in precision."  However, if I
leave filtering ON for crossvalidated analysis, is it
reasonable to set it OFF when do uncrossvalidated analysis?

Any suggestions or comments will be really appreciated. TIA!

Regards,

Jinsong

=====
(Mr.) Jinsong Zhao
Ph.D. Candidate
School of the Environment
Nanjing University
No.22 Hankou Road, Najing 210093
P.R. China
E-mail: zh_jinsong{at}yahoo.com.cn

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