DockoMatic is a free and open source application that unifies a suite of 
software programs within a user-friendly graphical user interface (GUI) to 
facilitate molecular docking experiments. Here we describe the release of 
DockoMatic 2.0; significant software advances include the ability to (1) conduct 
high throughput inverse virtual screening (IVS); (2) construct 3D homology 
models; and (3) customize the user interface. Users can now efficiently setup, 
start, and manage IVS experiments through the DockoMatic GUI by specifying 
receptor(s), ligand(s), grid parameter file(s), and docking engine (either 
AutoDock or AutoDock Vina). DockoMatic automatically generates the needed 
experiment input files and output directories and allows the user to manage and 
monitor job progress. Upon job completion, a summary of results is generated by 
Dockomatic to facilitate interpretation by the user. DockoMatic functionality 
has also been expanded to facilitate the construction of 3D protein homology 
models using the Timely Integrated Modeler (TIM) wizard. The wizard TIM provides 
an interface that accesses the basic local alignment search tool (BLAST) and 
MODELER programs and guides the user through the necessary steps to easily and 
efficiently create 3D homology models for biomacromolecular structures. The 
DockoMatic GUI can be customized by the user, and the software design makes it 
relatively easy to integrate additional docking engines, scoring functions, or 
third party programs. DockoMatic is a free comprehensive molecular docking 
software program for all levels of scientists in both research and education.