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.

Every structural biology course eventually hits the same wall: students can look at a folded protein in PyMOL, they can dock a ligand with AutoDock Vina, but they never actually see the physics doing the work. PyMOL doesn’t visualize forces. Vina’s scoring function is a black box unless you go digging through source code most students will never open. The intuition that molecular dynamics is just Newton’s second law, applied a few million times in a row, gets lost somewhere between the lecture slides and the exercise sheet.