PaDEL-ADV is a free and easy to use Java software to perform virtual screening using AutoDock Vina.
Before running PaDEL-ADV, you will need to do the following:
· Prepare receptor pdbqt file using AutoDockTools.
· Prepare AutoDock Vina configuration file with at least the following information (check AutoDock Vina manual for description of these information).
a) receptor
b) center_x
c) center_y
d) center_z
e) size_x
f) size_y
g) size_z
· Place all ligands files in a directory. Most common file formats (e.g. MDL mol, SMILES, PDB) and PDBQT files are supported.
· Run PaDEL-ADV, fill in all the fields and press the Start button. On completion, a zip file containing results and related files will be created for each ligand. The results from all the ligands will be consolidated into the specified CSV file.
Requirements:
· Java 6 or later
What`s New in This Release: [ read full changelog ]
· Change the way that the ligand.pdb, stored in the zip file, is generated in order to facilitate RMSD calculations.
