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16th June 2015 @ 13:05

The following 28 Malaria Box compounds, found to cause disruption against Na+ regulation in PfATP4  were used to search for common pharmacophore features.
 
Accerlys Discovery Studio was used running the Common Feature Pharmacophore Generation protocol.
 
Input Files
 
Protocol Parameter File
 
Protocol.pr_xml
 
Input SD file
 
Malaria_Box_active_clean.sd
 
Input SMILES and InChI codes
 
input_smiles.txt
 
 
The protocol produced 10 four-feature models, upon inspection of poses and score the following model was selected to be taken forward.
 
.CHM file
 
Malaria_Box_active_clean_03.chm
 
 
 

Fine tuning the model

The 28 active compounds aligned to the pharmacophore were used to create a shape feature that could be used to manually predict the shape of the active site.  10 exclusion features were then added in areas where high scoring, inactive ligands penetrated out of this shape.  The shape feature itself was never used as a query feature and was never intended to be used as such. 

 

03.png

04.png

05.png

06.png

Final CHM file

exclusion10_01.chm

 

 

 

 

 
 
Linked Entries
Attached Files
Protocol.pr_xml
Malaria_Box_active_clean.sd
input_smiles.txt
Malaria_Box_active_clean_03.chm
4-feature.PNG
03.png
04.png
05.png
06.png
07.png
Protocol.pr_xml
exclusion10_01.chm