Open source software tools for computer aided drug design

Abstract

Computer-aided drug design (CADD) has revolutionized the drug discovery arena and it has reduced the costs associated with finding novel compounds which are having pharmaceutical importance. In CADD, the scientists use the computer software to discover biological active compounds. Molecular docking and energy minimization tools are essential components of structure based drug design. It is a significant tool in structural molecular biology and computer-assisted drug design. It reduces the laboratory workload of the end user and allows researchers to restrict their docking studies to the smallest and the most representative set of macromolecules and small molecules possible. This greatly enhances the productivity of researchers. Energy minimization is an important criterion for selecting a potential 3D molecule. In modeled structures, the 3D structure is affected is due to steric clashes. These clashes happen in a protein structure due to the overlap of non bonding atoms and with the assistance of energy minimization, steric clashes can be eradicated. The open software’s and databases provides a platform for scientists and scholars to carry out their research work in a better way. The docking tools are discussed in this review cover protein-ligand, protein-peptide as well as protein-nucleic acid docking. The tools described include AutoDock 4 and Vina, UCSF DOCK, FLIPDock, EADock, HADDOCK 2.2, SwissDock, Patch-Dock and ClusPro. In addition to the docking tools, energy minimization tools such as YASARA minimization server, KoBaMIN server and 3D refine server have also been discussed. This mini-review concentrates on open software tools which are free of cost and can be easily downloaded in the computers that are useful for CADD.