I performed redocking to validate my docking procedure. First, I removed water and then extracted the protein (PDB ID: 3BPF) and ligand into separate pdb files, followed by adding polar hydrogens to both protein and ligand. However, the ligand conformation is not the same as seen in the crystal conformation. So what is the actual procedure when performing redocking?
In Autodock Vina config.file I used is exhaustiveness = 10 and energy_range = 9. Actually i already manipulated the settings few times but still fail to get desired conformation.
The green ligand is the conformation seen in pdb file while the blue ligand is the conformation of re-docking.
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Hi Wei,
You should add hydrogens to your protein by use of PDB2PQR server or UCSF Chimera, and then convert pdb file format to pdbqt by AutoDock Tools.
http://nbcr-222.ucsd.edu/pdb2pqr_2.1.1/
https://www.cgl.ucsf.edu/chimera/
Yoshinobu Ishikawa This might sound like a stupid question but I am a beginner in this field. So do I need to add hydrogens to my ligand as well in PDB2PQR /UCSF Chimera or just adding polar hydrogens in Autodock Tools as show in the Autodock Vina tutorial?
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