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SEA, the similarity ensemble approach.
#REDIRECT [[Category:SEA]]
[http://sea.docking.org sea.docking.org]
 
[[Install SEA]]
 
[[Basic Tutorial]]
 
[[Chembl processing protocol]]
 
 
== How to generate a model to run SEA ==
 
We need the files: reference.smi ; reference.set ; reference.fp
 
First we need to generate the background Z-score distribution:
 
[prompt]$ sea-background reference.set.gz
 
This generated the file model.out
 
Then we need to fit data the data from this background model and build a fit parameter file:
 
[prompt]$ sea-fit model.out
 
This generates the file model.out.distfit, containing the values for the best fit of the background distribution to a normal and an extreme value distribution. From this distribution, we need to select the optimal cutoff and then use it to get the fit file.
 
[prompt]$ sea-fit -c cutoff model.out
 
 
[[Category:SEA]]
[[Category:Scaffold hopping]]
[[Category:Off target effects]]
[[Category:Pharmacology]]

Latest revision as of 08:03, 13 March 2014

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