Scaffold Hunter heads to Google

16 October 2013

Scaffold Hunter screen shot
Scaffold Hunter screen shot

The University of Sydney researcher behind Scaffold Hunter, prize-winning open source software, has been invited to attend the Google Summer of Code (GSoC) Mentor summit held in San Francisco, USA.

Dr Karsten Klein, a senior research fellow in the Faculty of Engineering and Information Technologies initially designed Scaffold Hunter seven years ago while working at the Technical University Dortmund. He will present Scaffold Hunter as one of the open source projects for this year's GsoC program.

Dr Klein says the invitation from Google was a great honour for the University's School of Information Technologies.

"Google's GSoC supports world-class open source software development by sponsoring students from all around to world to contribute to the software. It's exciting to work with both our students and those from other universities, as well as with Google."

Scaffold Hunter was recently awarded the best software prize at the OpenTox Euro 2013 InterAction conference at Johannes Gutenberg University of Mainz, in Germany.

"Scaffold Hunter started as a collaboration with the Max Planck Institute of Molecular Physiology," explains Dr Klein.

"Our main goal was to have a tool that allowed visual analysis of chemical compound data to find potential drug candidates quicker and with a higher quality than standard trial-and-error methods.

"The classical drug discovery pipeline, which aims at detecting small molecules that bind to biological target molecules that are involved in a disease process, such as proteins, not only requires a large amount of time, money, and other resources, but also suffers from a small and decreasing success rate.

"We initiated a large one year student project to realise a prototype." he says.

The project's results were published in the prestigious international journal Nature Chemical Biology.

Dr Klein now leads a student research team at the University of Sydney. The team continues to develop Scaffold Hunter in collaboration with colleagues in Germany and is addressing its ability to meet an increasing demand for chemogenomics in drug development.

"Chemogenomics is concerned with the systematic analysis of chemical-biological interactions, with the goal to identify new drugs or drug targets. There are an almost infinite number of drug-like organic molecules which can potentially be discovered."

"The amount of data gathered has increased exponentially, as has the demand for its analysis. Scaffold Hunter is an accessible, Java-based application built for the analysis of structure-related biochemical data."

The program facilitates the interactive exploration of chemical space. It provides a guided navigation based on a hierarchical molecule classification called scaffold tree that allows the user to quickly identify regions of high probability for potential drug candidates.

Scaffold Hunter is also an ideal base from which to implement a solution for wider applications. By collaborating with medical imaging researchers in the faculty, Scaffold Hunter has been expanded to a visual analytics approach to medical image retrieval

Dr Jinman Kim, Biomedical Imaging Theme leader of the faculty's Institute of Biomedical Engineering and Technology (BMET) says:

"Scaffold Hunter enables the combination of automated analysis of medical image data with interactive visualisations, allowing a person to use their expertise and intuition to make new findings where automated analysis alone would fail as the task and data would be too complex to solve."

Media Contact: Victoria Hollick, 02 9351 2579, 0401 711 361,