I would like to perform the docking with Ligandfit Protocol of Discovery studio 2.1.
Please let me know the procedure regarding the control ligand input.
My current input receptor is 1J8J from pdb. Structure of plasmepsin of plasmodium falciparum and my personal ligand library already prepared.
Please give detailed information regarding this.
Thanking you.
To run a Dock Ligands (LigandFit) protocol
Load the Receptor-Ligand Interactions | Dock Ligands (LigandFit) protocol from the Protocols Explorer. The parameters display in the Parameters Explorer.
Load the structure you want to define as the receptor into the Graphics View.
Define the Input Receptor by selecting the receptor from the dropdown list of molecules. The receptor must have hydrogens added and all atom valencies satisfied so that atoms can be properly typed.
Open the Define and Edit Binding Site tool panel and click Define Selected Molecule as Receptor.
If not site is present click on Find Sites from Receptor Cavities in the Define and Edit Binding Site tool panel to calculate the binding sites.
On the Parameters Explorer, select a binding site from the list of all sites found for this receptor in the Input Binding Site parameter.
On the Parameters Explorer, use the Input Ligands parameter to specify the ligands.
Adjust the ligand flexibility by changing the Conformation search Number of Monte Carlo Trials parameter. Click the button to launch the Monte Carlo Trials dialog, which allows you to specify rigid docking, fixed, or variable number of Monte Carlo steps for varying torsion numbers.
Set the remaining parameters as desired. Parameters presented in red are required.
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