D2MD Suite is a collection of applications that attempts to help automatizing and batch processing the molecular docking studies of DNA-Drug complexes.

A simple GUI to the AutoGrid and AutoDock programs, in the case the AutoDockTools GUI is too buggy also for you.

Requirements:
· Java 6
· AutoDock 4.2

Vina Helper
Starting from an AutoDock 4.2 grid file and the ligand PDBQT, this program allows you to perform a docking simulation by AutoDock Vina without having to build any configuration file or recalculate any grid.

Requirements:
· Java 6
· AutoDock 4.2
· AutoDock Vina 1.1.2

Output of AutoDock and Vina simulations can be analyzed better with these tools, by doing a mean on all conformations or on a particular RMS cluster set.

Requirements:
· Java 6
· AutoDock 4.2
· AutoDock Vina 1.1.2
· MGLTools 1.5.6rc2

This programs is a full featured DNA-Drug Vina docking simulation. It's completely automatized since starting from the ligand and DNA PDB files one needs only to select one of the automatically discovered intercalation spaces (or none if blind docking) and start a simulation.

Requirements
· Java 6
· Java 3D 1.5.2
· BioJava 3.0.2
· AutoDock Vina 1.1.2
· MGLTools 1.5.6rc2

D2MD Suite is a cross-platform utility capable of running on any operating system that comes with Java support (e.g. Mac OS X, Windows, Linux).