1.Atomistix ToolKit (ATK) offers unique capabilities for simulating electrical transport properties of nanodevices on the atomic scale. Based on an open architecture which integrates a powerful scripting language with a graphical user interface, ATK is a comprehensive platform for studies in nanoelectronics, using both accurate first-principles (DFT) and fast semi-empirical methods and classical potentials. Moreover, ATK includes a very advanced electrostatic model to allow realistic simulations of nanoscale transistor structures.

2.AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. AutoDock Vina is an open-source program for doing molecular docking. It was designed and implemented by Dr. Oleg Trott in the Molecular Graphics Lab at The Scripps Research Institute.

3.UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories and conformational ensembles. High-quality images and animations can be generated.

4.DOCK addresses the problem of “docking” molecules to each other. In general, “docking” is the identification of the low-energy binding modes of a small molecule, or ligand, within the active site of a macromolecule, or receptor, whose structure is known. A compound that interacts strongly with, or binds, a receptor associated with a disease may inhibit its function and thus act as a drug. Solving the docking problem computationally requires an accurate representation of the molecular energetics as well as an efficient algorithm to search the potential binding modes.