The following tutorial is also available in .pdf format tutorial.pdf
Here, we aim to find molecules that belongs to the molecular weight range [0 - 469], possess a carbonyl and a F sybyl atom type (= a fluorine ; see the pharmacophore property). The case is trivial but it allows the test to be rapidly executed. The de novo drug design is time consuming especially when the scoring function involves the docking program.
Note that the program uses a heuristic method and may not found an exact solution. Each run will produce a different solution.
Select AMBER options in "Pick a forcefield" and "Pick an output naming scheme"
Set the option "Add/keep chain IDs in the PQR file"
Launch the execution
Download the .pqr file and rename it with the extension .pdb. The protein has been protonated and formatted with AMBER naming scheme
Be careful, heteroatoms like ligands are removed. In such case and if needed (for example, in defining the binding site), copy the ligand coordinates from the original file at the end of the pqr.pdb file.
Get the output from PQR and copy/paste the HETATM 9RA block from 3H0A.pdb in the downloaded file: 3H0A_pqr.pdb
The above docking form must be filled with:
RESIDUE name= 9RA
RESIDUE number= 500
CHAIN name= A
Binding site radius= 10
Weight in final score= 1
Download the sdf format of the ligand 9RA: bexarotene.sdf in order to evaluate it (the form appear 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