Molecular Docking

Abstract

Molecular docking (MD) is one of the commonly used method to predict the orientation of two molecules bound in a stable complex. Elucidation of knowledge about the preferred molecular orientation helps in predicting the binding affinity between two test molecules. MD is the most widely used method in structure-based drug designing and also in biochemical investigations. There are two major steps involved in MD procedure: first is a search algorithm and second is a scoring function. The search algorithm can differentiate between conformational changes of the ligand through one of the techniques above, while scoring function usually classifies different shapes retrieved by the search algorithm. The most widely used computational programs in docking procedure are DOCK, GOLD, AutoDock, Surflex, FlexX, FTDOCK, etc. These methods differ from each other in implementation of the search algorithms and their scoring function differences. In this current chapter we demonstrated the molecular docking working procedure using an easily accessible and easy-to-use AutoDock software. A brief description of different experimental stages and interpretation of results are explained with the help of different screenshots.