LEA3D offers a facility to screen or to design small molecules
The user first builds a scoring function and then, at the second step, either uploads a library of molecules or selects the de novo drug design option
The FDA-approved drug structure data set can be selected at the step 2
Set the docking function
(*) mandatory fields
It is recommended to associate the docking function with an upper limit for the Molecular Weight (MW<500 for example; see the "select properties" function below) to speed up the calculation because this will discard large molecules before the docking.
Calculate molecular shape similarities with a reference molecule
(*) mandatory fields
Select properties
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 (tool to prepare protein input files).
Help:
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).
How to set property values:
Example 1: set the minimal value only
Molecular weight
100
-
1.0
Means MW must be ≥ 100
Example 2: set the maximal value only
Molecular weight
-
469
1.0
Means MW must be ≤ 469
Example 3: set the minimal and the maximal value with the same value
Molecular weight
100
100
1.0
Means MW must be exactly 100
Example 4: set the minimal and the maximal value with different values
