Case Study: Max Planck Institute of Biochemistry achieves accelerated 3D protein reconstruction and cuts years off research with MathWorks

The Max Planck Institute Reconstructs Key Protein Complexes

The Max Planck Institute of Biochemistry faced the challenge of reconstructing high‑quality 3D structures of fragile protein complexes—most notably the unstable 26S proteasome—by averaging millions of noisy 2D cryo‑EM projections. To handle massive datasets and complex image‑processing tasks, the institute turned to MathWorks tools including MATLAB, Image Processing Toolbox, Parallel Computing Toolbox, Statistics and Machine Learning Toolbox, and MATLAB Distributed Computing Server.

Using MathWorks software, researchers built a single‑environment workflow: a MATLAB GUI to automate image acquisition, Image Processing Toolbox to correct contrast transfer effects, Statistics and Machine Learning Toolbox for classification (PCA and self‑organizing maps), and Parallel Computing Toolbox with their cluster to accelerate computation. MathWorks’ tools enabled 20–30× speedups (reducing week‑long jobs to overnight), cut development time from weeks to days, and produced a highest‑resolution 26S reconstruction in under two years where previous efforts had taken nearly a decade.

Max Planck Institute of Biochemistry

Andreas Korinek

Scientist