Molecular Docking | Autodock VINA Virtual Screening | VINA Docking tutorial | Bioinformatics

Virtual screening based on molecular docking is becoming a powerful tool in identifying lead compounds in a huge pool of small molecules.After the construction of library and preparation of receptor, each compound in the library is virtually docked into the target binding site with a docking program.
The Docking aims to predict the ligand-protein complex structure by exploring the conformational space of the ligands within the binding site of the protein. A scoring function is then utilized to calculate the free energy of binding between the protein and the ligand in each docking pose or confirmation. Docking and scoring produce ranked compounds, which are then post-processed by examining calculated binding scores, validity of generated pose, undesirable chemical moieties, metabolic liabilities, desired physicochemical properties, lead-likeness, and chemical diversity.
Post-processing results can filer down the compounds, which can be further proceed to experimental assay to identify potential compounds.

AutoDock Vina significantly improves the average accuracy of the binding mode predictions compared to AutoDock 4.

MGL Tools: http://mgltools.scripps.edu/
Autodock Vina: http://vina.scripps.edu/index.html
OpenBabel: https://bit.ly/3eMgXZm
Perl: http://padre.perlide.org/

PerlScript File: https://bit.ly/31gNgef


Literature:
https://www.nature.com/articles/s4159...
https://pubmed.ncbi.nlm.nih.gov/28809...
https://experiments.springernature.co...