About Me


I’m Timo Strunk and this is my CV (Update April 2013).

If you want to know who I am, you have to know my work. From my late school years on, I knew I wanted to do something, which has impact on the world; that is solve a problem, help the people. I also knew that I was alright with math and programming. Studying physics seemed appropriate for grand dreams and hence I studied it and love it ever since. Although my passion studying physics was basically theoretical (and analytical) physics, my aims pulled me towards the ‘dirty’ side of biophysics.

From here on out I worked on protein structure prediction and protein interactions hoping to pull the field of protein simulation from lottery to a field of engineering. While we and also fellow groups (Bakerlab – Rosetta@Home), (Zhang Lab – ITasser), …  showed a lot of progress in the recent years, currently there is no single secure method of predicting protein structure even for small proteins like peptides (without structural information of other proteins). If we had such a tool, we could finally start designing proteins from scratch; this is what I would call engineering: Giving engineers a toolkit like a CAD program, where they could build protein structures using Protein Structure Prediction, knowing when a segment will be stable and when not. On my way to this goal I developed the BOINC server POEM@HOME as part of my diploma thesis in the group of Prof. Dr. Wolfgang Wenzel and also folded some proteins from scratch with the help of many POEM@HOME volunteers and the simulation package jpoem, an already existing Monte Carlo simulation package implementing PFF02.

It was obvious that we need a more flexible tool to achieve folding of bigger proteins from scratch; therefore I implemented SIMONA from scratch with the help from many members of my group, especially Moritz Wolf. It has a versatile XML command language and is also used not only for protein simulation but also for general Nanosimulations. Now that we have the infrastructure (POEM@HOME) and the tool (SIMONA) it’s time to start stabilising the native conformations. This is where my phd started (in the same group). Funded by the Carl-Zeiss Foundation I developed a protocol in SIMONA for absolute quality assessment of protein structures. Our theory is simple: Native protein conformations are marginally stable; therefore every amino acids should also reside in a stability region energy-wise. I developed a statistical test to probe for these stability regions from a single structure alone. I finished my Ph.D in November 2012 (publication pending). The program SIMONA itself is available at SIMONA

These are my publications, proceedings, talks: Link They are also listed on my group’s site, but there they may be a bit outdated: Link.

So this was my ‘corporate’ me. Apart from my work, which actually defines a big part of my life, I live with my adorable girlfriend in Karlsruhe, enjoy going out with my friends, enjoy lots of video-games, enjoy fixing PCs for my friends and do the usual stuff. I also boycott social networks, as I was basically always on ICQ and IRC, which sufficed for my social needs. Apart from that I definitely enjoy following some ideas for start-ups, 1 per week, which up until now didn’t leave the blueprint stages.

But who knows…

 Posted by at 5:20 pm

  2 Responses to “About Me”

  1. Hey Timo.
    Schön zu sehen, dass es dir gut geht. Und vor allem interessante Arbeit.
    Viel Glück

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