Most in silico DTBA prediction procedure developed to date use 3D structural information, DTBA(drug target binding affinity) signs the strength of the interaction or binding between a drug and its target which was demonstrated to successfully contribute to the drug design. The 3D structure information of proteins is used in the molecular docking analysis which followed by applying search algorithms or scoring functions to comfort with the binding affinity predictions and this whole process is used in the structured-based virtual screening. The benefits of formulating drug-target prediction as a binding affinity regression task, is that it can be transformed from regression to either binary classification by setting specific thresholds or to ranking problem Even though the macromolecular structure and small molecule databases are an essential factor for drug discovery in silico, but it still needs the effective software for performing virtual screening on targets and small molecule databases, the computer-aided software has successfully applied into virtual screening studies and accelerated the process of drug discovery. Usually, the computational methods for drug discovery can be divided into ligandbased (indirect) and structure-based (direct) technique is the ligand-based drug design methods contain quantitative structure-activity relationship (QSAR), pharmacophore, etc. and the structure-based drug design contains molecular docking. The computer-aided software has successfully applied into virtual screening studies and accelerated the process of drug discovery. AutoDock, has faster run speed and more accurate binding mode predictions than AutoDock62. MD software can be used to study the dynamical interaction between targets and ligands at the atomic level. It can profile more detail and accurate interaction information for ligands in the pocket of receptor than molecular docking , and this MD simulations have become the popular method to study the mechanism of activated, inactivated states and ligand interaction on different targets, such as ion channel receptors, etc.