Software from the Structural Biology Programme at the Spanish National Cancer Research Centre (CNIO), Madrid.
We build and maintain the tools we use every day: cryo-EM data collection and processing, protein design, biochemistry data analysis, and web apps that help us run things in the labs. Everything public here is released for the community to use and adapt.
BinderFlow — an automated, modular pipeline for de novo protein binder design on SLURM clusters. Runs backbone generation, filtering, sequence design and scoring in batches, with BFmonitor, a web dashboard for live campaign monitoring and hit selection. Built on RFdiffusion, dl_binder_design and PyRosetta.
CNIO_Relion_Tools —
web-based dashboards for RELION 5: relion_live.py for real-time feedback
during data collection, relion_analyse.py for interactive analysis of project
metadata (2D/3D classification, refinement convergence, particle statistics),
plus ice-thickness estimation and parallelised PNG export.
RELION_ShiftParticles2D — RELION external job that re-centres particles after 2D classification using the centre of mass of each class average or a user-provided shift.
CE_tools — processing pipeline
for capillary electrophoresis data from primer-extension DNA assays: .fsa
extraction, normalisation, peak quantification, statistical reporting and an
interactive Dash dashboard.
SBP-APPS — some of the programme's web apps and dashboards people are developing to carry out their everyday work, served at cryoem-cnio.github.io/SBP-APPS.
If our tools are useful in your work, please cite them:
BinderFlow
González-Rodríguez N, Chacón-Sánchez C, Llorca O, Fernández-Leiro R. Automated and modular protein binder design with BinderFlow. PLOS Comput. Biol. 21(11), e1013747 (2025). https://doi.org/10.1371/journal.pcbi.1013747
relion_live.py / relion_analyse.py (CNIO_Relion_Tools)
González-Rodríguez N, Areán-Ulloa E, Fernández-Leiro R. A web-based dashboard for RELION metadata visualization. Acta Cryst. D 80, 93–100 (2024). https://doi.org/10.1107/S2059798323010902
Issues and pull requests are welcome on any of the public repositories. If you hit a problem or want a feature, open an issue, we read them 🙂
Rafael Fernández-Leiro [email protected] · Genome Integrity and Structural Biology Group · CNIO