[Dock-fans] False positives

Gustavo HMF Souza koraxgh at gmail.com
Thu Mar 29 13:06:53 PST 2007

Hi ! (Scott)!

After rescore with AMBER, many ligands appears to be near active site - the
selected_spheres, but they are not inside them like the specific ligand (as
a positive control). Ok. Until now everything is all right, therefore, after
AMBER these ligands does not have a negative score. All of them, including
those that are outside the selected spheres, have almost the same score!!???
How can I fix this ? I think that calculations is everything wrong! Please I
need a help!!
Now I have some questions:

1- Can I affirm that positive AMBER score means inhibition? Or substrates?
If inhibitor why?

2- Why my score after dock calculations with a specific knowing ligand with
a high Ki is lower than another with  a lower Ki? Please I need help ... If
is the problem is not clear, Can I send some input/output problem files to
you ?

3- How can I interpret the data from AMBER (negative score -don`t bind;
positive score -means bind)????????????

3- How can I plot the data coming from AMBER score like the tutorial
(showing the decoys and binders)?

With all my best, (and urgent!)
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