![]() If you have downloaded smiles and want to convert them into 3D conformers then again use OpenBabel for that. You can also use OpenBabel software to convert them from sdf into pdbqt format. Prepare pdbqt files of the target protein and all ligands. (Video tutorials: site-specific docking and blind docking). The docking procedure will be the same as mentioned in previous articles on site-specific docking and blind docking. In this article, we will use a Perl script or a bash script to screen several ligands for a target protein. You can simply load your target protein and ligand pdb files. These plugins provide a graphical user interface and there is no need to prepare pdbqt files of protein and ligands. In previous articles, we have provided tutorials for the installation of Raccoon and Raccoon2 plugins on Ubuntu. Recently, Autodock Vina has provided plugins to facilitate virtual screening. Autodock Vina is a freely accessible software and provides good results can also be used for screening various ligands. There is various software available for virtual screening including GOLD and GLIDE. Virtual screening is used to identify small molecules that are most likely to bind to a target protein.
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