Cheminformatics: Your Personal Ticket Into the Thriving Biotech World?

Just 10 years ago, bioinformatics was a term unknown even to fortunetellers. Now there's a fascinating new field emerging called cheminformatics. Andreas Bender, a chemistry student in Berlin, tells you how he got into the new field and what it is all about.

I started my studies of chemistry in Berlin just 3 years ago. It didn't take too long for me to realize there's one thing I don't want to see again--labs. I realized that it's not my field, and at the same time I started to become fascinated by simulation methods. I began to like the idea of predicting reality by devising algorithms, implementing them--and getting a result that tells you what will happen and how things in real life will look like. You can understand the three-dimensional structure of a molecule without taking an x-ray, and you can predict whether a certain molecule will bind to a given receptor--I was really excited about those ideas.

Then I spent a year in Ireland, at the chemistry department of Trinity College, Dublin, where I was doing computer simulations for the first time. As part of the study, we tried to predict the structure of an inorganic cluster. When the experimental structure was determined a few weeks later, we found that our prediction was right, the cluster really looked like our computer had predicted! The year at Trinity was over soon, and a new idea came into my mind--how about using computer simulations and applying them to biological systems?

Back in Germany this spring, I decided to use the 3-month summer break of German universities to get some experience in this field and started looking for a position as a summer intern in a biotech company. Also, I wanted to work in a young, thriving company, preferably a start-up. There are some platforms on the Web which are offering firms the possibility to place ads for interns, and at a student magazine's Web site I found the perfect match for my interests in an ad from CallistoGen, located in Hennigsdorf on the outskirts of Berlin.

This 1-year-old company develops active substances for medical treatments and especially uses computational methods for achieving this. And I don't exaggerate if I say that they were "thriving"--as my expectations were. I met young and uncomplicated people, most of them just 30 and from university, where I felt comfortable. They were from all over the world and they didn't employ just scientists in the traditional sense, the criterion was knowledge and capability, for example they also employed some engineers.

In that company I joined the "cheminformatics" group and worked mainly with a new tool trying to predict the binding activity to given receptors. Special about that tool was that you did not need to know anything about the receptor the ligand binds to, and especially you don't need to know the structure, which is often very difficult to determine experimentally. You need some active molecules, and this tool finds molecules that possess similar binding affinities to the same receptor. That's a huge advantage. Instead of screening hundreds and thousands of substances in experimental tests, you can narrow down your search to some molecules that are "probably" active.

When I joined the company, the cheminformatics tool was already up and running--but nobody knew the best way to really use it. The first results were promising, but there were several parameters that had to be optimized. The bad thing was that when you change one of the parameters, you see that all the others depend on this one. It became my task to program several tools for data analysis. I also wrote tools for visualizing the output and helped to make this tool even more valuable and far better understood than before.

I am still working for this company part-time, now that my dream of using computational methods for drawing conclusions "for reality" has come true. So, if you are a chemist and like simulations--why not try using your knowledge and working in a young start-up, developing tools which will be used for "intelligent" discovery of new pharmaceutical compounds? You will certainly find an inspiring atmosphere and enter a field with the brightest prospects.

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