YSBL logo Vernalis corporate website rDock home page University of York, Biology Department
Home Obtaining Documentation Ancillary programs Support Test Data Links Contact

Ancillary Programs to Complement the rDock Platform

Here you can obtain additional programs and tools for the rDock platform. The programs here are not vital to the running of rDock, but may make various tasks easier to perform. As an additional note, the programs listed here require that a working copy of rDock is installed on your system.
 
Graphical User Interface (GUI) [zip] [tar.gz]
 
    This GUI was created in JAVA to complement the rDock command line interface and provide better user-friendliness for those less comfortable with the linux terminal. Starting with a .pdb file and a ligand the GUI allows the user to check them for errors that may effect the docking proceedure, such as disorder and missing atoms, and also allows the user to view their protein/ligand within the freely available Discovery Studio (DS) Visualizer molecular visualization tool (for more information on DS Visualizer see the Links section).

    With the molecule and ligand checked the GUI then generates the cavity where docking will take place using internal scripting. From there docking can begin, either using the predifined docking protocol or one imported by the user. The results (docking scores) are returned as an output file in .sd format, which can be read by any 3D molecular visualisation software such as DS Visualizer.

    For a more detailed coverage of the GUI's functions and usability there is a user manual available here in pdf format and within the archive containing the GUI.