COMPARATIVE EVALUATION OF PROTEIN AND LIGAND-BASED DOCKING PROTOCOLS THROUGH PROTEIN PHOSPHATASE SLINGSHOT HOMOLOG 2 COMPLEX

Abstract

A molecular docking study is used to investigate the interactions between the two molecules. These interactions may be covalent, hydrogen, or Van der Waals forces. Various web-based and stand-alone tools have been discovered for molecular docking analysis. In this study, we performed a comparison between web-based and stand-alone docking tools to evaluate the accuracy. Five web-based tools i) Dockthor, ii) Patchdock, iii) RPBA Web, iv) Swissdock, v) Patinum and two stand-alone tools1) Autodock Vina & 2) Hex were selected for the evaluation of the tool`s accuracy in term of best conformations with minimum binding energies. Protein phosphatase Slingshot homolog 2, SSH2 (PDBID: 2NT2) and four of its related proteins were used as the key proteins in this study. Ligands and Proteins interacting with SSH2 in the Novel signalling pathway were investigated through above mentioned tools.