First step: Fill the scoring function form and Submit
Fill the following form to screen a database of molecules or to use the de novo drug design program.
The field "Weight in final score" must be different from 0 in order to activate the individual function.
Define the docking function
It is recommended to associate the docking function with an upper limit for the Molecular Weight (MW<500 for example) to speed up the run, particularly if you chose the de novo drug design option.
Define the molecular-based function
Preparation of the protein file for PLANTS
The program PLANTS needs a .mol2 protein file format thus our procedure automatically protonates the uploaded .pdb structure file by using the program PDBPQR with AMBER forcefield option. Then, the pdb file is converted into a .mol2 file format.
Example of the protein used in the automatic test (pdb 3H0A):
Download the sdf format of the ligand 9RA: bexarotene.sdf in order to evaluate it (the form appears at the second step (html page after the submit))
Help to set molecular properties:
The final score is the sum of each selected property. The score is expressed in percentage (%) where each selected property contributes proportionally to its weight (ie. ∑(weighti) → 100% with i a selected property).
Example 1: set the minimal value only
Means MW must be ≥ 100
Example 2: set the maximal value only
Means MW must be ≤ 469
Example 3: set the minimal and the maximal value with the same value
Means MW must be exactly 100
Example 4: set the minimal and the maximal value with different values