Directed synthesis and data analysis tool

OOMMPPAA is a novel computational tool designed to inform compound design by combining structural and activity data. OOMMPPAA uses 3D matched molecular pairs to contextualise both activity and inactivity data in its relevant protein environment. It then identifies pharmacophoric transformations between pairs of compounds and associates them with their relevant activity changes. OOMMPPAA presents this data in an interactive application providing the user with a visual summary of important interactions in the context of the binding site.

Online: you can try out the functionality using openly available CDK2 data

Offline: for using your own datasets we have developed standalone executables. The inputs are (A) a file of complexed ligands, and (B) activity data. The output is a 3D display of all pharmacophoric changes between molecules.

This work is based on the following paper in submission:

I am a DPhil candidate at the University of Oxford. I work between the Structural Genomics Consortium (SGC) and the Oxford Protein Informatics Group (OPIG) for short.

I am sponsored by GlaxoSmithKline and work with their Computational and Structural Chemistry department, developing tools to improve data analysis.

Contact me at oommppaa.help@gmail.com, or view my webpage at Anthony Bradley

You require the ActiveICM plugin


Download the package here

64 bit IE requires this EXTRA package


NOTE that gtkglext package is required. Instructions here

64 bit download the package here

32 bit download the package here

Install instructions here


Mac download the package here

Any poblems e-mail the mailing list: oommppaa.help@gmail.com

Get Started Skip tutorial

Interactive and responsive UI

We have built an interactive and simple UI for OOMMPPAA to aid non-experts in using the tool. Just have a go! OOMMPPAA is built on the twitter bootstrap web framework, meaning it will look beautiful on any screen.

Use your own data

We have gone to great lengths to make the tool easy to install for your own use. Install the software and run it on your own data.


Because OOMMPPAA is written in python, it is cross-platform. We have installed OOMMPPAA on Mac, Windows and Linux. Use our wikis to help you out.

No dependencies required

We have made a one click installer for Windows users. No need to install python or any modules. Also no need to worry about module version conflicts, OOMMPPAA comes completely self-contained. A mac equivelant is in the pipeline.

Scalable for departmental use

OOMMPPAA is based on Django, which is designed for scalable use. We give full instructions in setting up a robust stack, using modern web-technologies (nginx, gunicorn and django).

You can install OOMMPPAA on your own machine. This allows the tool to be used on your own data and without being connected to the internet.

Any poblems e-mail the mailng list: oommppaa.help@gmail.com


We have developed a windows installer for one click access and NO depednecies.


  • OOMMPPAA has been installed and tested from source on linux
  • Full instructions for installing on Ubuntu Linux 12.04 LTS are available in this Wiki

  • Instructions include those for making a robust NGINX, gunicorn, Django stack for site-wide use are shown in this Wiki


  • OOMMPPAA has been intalled and tested from source on MacOSX
  • Full instructions for installing on Mac can be found here in this Wiki
Bitbucket Windows