pharmine

Introducing another new software, PaDEL-ADV. This is a software to perform virtual screening using AutoDock Vina.

PaDEL-ADV reads a directory containing ligands files. For each ligand, the structural file is converted into a pdb file, if necessary, using The Chemistry Development Kit. The pdb file is then converted to pdbqt using the prepare_ligand4.py script provided by AutoDockTools. AutoDock Vina is then used to dock the ligand with the receptor. Individual binding modes are extracted from the output pdbqt file using vina_split. The pdbqt files are then converted to pdb files using the pdbqt_to_pdb.py script provided by AutoDockTools. Results for each binding modes are extracted from the log file and placed into the results CSV file. The log file and all the related pdb and pdbqt files are then compressed into a zip file.

This entry was posted by Yap Chun Wei on Monday, November 9th, 2009 at 11:53 pm and is filed under Java, Pharmacy. You can follow any responses to this entry through the RSS 2.0 feed. You can leave a response, or trackback from your own site.