Numerical Methods of Cryo Electron Tomography Laboratory

Group leader
Daniel Castaño

Biofisika Institute (CSIC-UPV/EHU)
Science Park of the UPV/EHU
Barrio Sarriena s/n. 48940 Leioa, Bizkaia (Spain)

Research goal

We develop software and algorithmic methods for cryo-electron tomography (cryoET). Our inhouse package Dynamo covers all stages of this computational pipeline: alignment of tilt series, reconstruction of tomograms, particle extraction and subtomogram averaging and classification. Using constitutive exocytosis in yeast cells as experimental example, we ultimately aim at building a numerical infrastructure for the combined use of cryoET, intracellular nanotools and live cell imaging to resolve dynamic cellular processes with atomic resolution.

Group members
CSIC Scientist

S Scaramuzza, D Castaño-Díez.

Step-by-step guide to efficient subtomogram averaging of virus-like particles with Dynamo. PLOS Biology. 2021 Aug 19(8): e3001318. PMID: 34437529.
DOI: 10.1371/journal.pbio.3001318

PP Navarro, H Stahlberg, D Castaño-Díez.

Protocols for subtomogram averaging of membrane proteins in the Dynamo software package. Frontiers in molecular biosciences. 2018 Sep 4;5:82. PMID: 30234127.
DOI: 10.3389/fmolb.2018.00082

D Castaño-Díez, M Kudryashev, H Stahlberg

Dynamo catalogue: geometrical tools and data management for particle picking in subtomogram averaging of cryo-electron tomograms. Journal of Structural Biology. 2017 Feb;197(2):135-144. PMID: 27288866.
DOI: 10.1016/j.jsb.2016.06.005