Hi all

I have three questions:

1. The equation used to identifying lead compounds in pharmacophore modeling is

                                               MA*uncert - A/uncert > 0 -------------------------(1)

and for inactive compound removal is

                                               A/MA > 10^3.5.-----------------------------(2)

Assuming that the activity of the unknown ligand is m times numerically higher than that of the most active ligands [numerically and not logically. i.e A = m * MA ] and hence solving these two equations, simultaneously we get

      m > 10^ (3.5) or m > 3163 AND plugging the value of m in equation (1) results in (uncert)^2 - m > 0 OR uncert > SQRT( m ) = 56.

The question here is in the protocols, it is said that uncert value is chosen as 1.5, why and and under what basis

2. Is it possible in discovery studio to frame the rules (eqn 1 and 2) manually instead of letting the software to work on it. I would particularly like to change the value of the ratio in equation (2)

3. How do we get a 2D image of the pharmacophore along with its features and feature distances.