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Support for the rDock Platform

This support information is intended to be supplemental to the documentation supplied in the user guides.
How do I get started?
Try Tutorial 1 which is designed to help you get started with rDock. A more in-depth getting started guide is available from the documentation page.

Will it work with Windows?
This program has been solely designed to run under linux and has not been tested using Windows. There are no plans to make a version for Windows.

Does it cost anything to use?
No, it is completely free, but please read the End User License Agreement for the terms and conditions associated with use of rDock.

How do you calculate the scores?
The details of the algorithms used to calculate the scores are found here.

Will it work with PDB files instead of MOL2 files?
mol2 files are necessary as they contain more specific information relating to the distributed charges in the compound. While this can be inferred from PDB files it is not as accurate and must be done manually. If you have a pdb file, programs such as DS Visualiser are capable of converting this to a mol2 file when you save it.

Can I input a list of ligands instead of just one at a time?
This is something we are working on at the moment. We hope that in the near future it will be possible to input files through the GUI which contain more than one ligand. However, at the moment this is not up and running.

Can I view a sample/test without installing the program?
Here is a sample of the output generated by rDock. It is an .sd file which can be viewed with properly with most 3D molecular visualisation software.It will open in a new web browser window in text format. To view it properly, save it as an .sd file and open with your chosen visualisation software.

I would like to be kept informed of updates. Do you have a mailing list?
We do not have a mailing list. All updates will be posted on this website and on our forum.If you have any specific queries please email us at rdock@ysbl.york.ac.ukor discuss them on our forum

Is there a resource containing pre-formatted ligand files I can use to screen with my protein?
We are working on formatting a database containing a large number of pre-formatted ligands. It will be made available on this site as soon as it has been fully tested.

Is it compatible with visualisers other than DS Visualiser?
Yes, the .sd files which are given as the output should be compatible with most 3D molecular visualisation programs.

Can I run this without using the linux command line?
You will have to set this up using the linux command line as it needs to be compiled before it will run. However, after this you can do most things using the GUI. You can download this from the ancillary programs page on this site, and there is also a tutorial on how to use it available on the support page.

Tutorials covering the implementation of the rDock platform.