Structural Bioinformatics

I’m part of the teaching team for the Bio Data Science program’s structural bioinformatics course at FHWN, split across the Wiener Neustadt and Tulln campuses. The materials I write for it live at structural-bioinformatics-exercises, and this post isn’t really about the repository — it’s about the idea that shaped it.

In a structural bioinformatics course, students look at proteins in PyMOL and dock ligands with AutoDock Vina, but neither tool shows them the forces involved. PyMOL doesn’t display forces, and Vina’s scoring function is hard to inspect without reading its source code. The idea that molecular dynamics is Newton’s second law applied many times in a row is easy to state in a lecture and hard to see in practice.