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is a collection of Python scripts for manipulating Relion tomo STAR files and performing various cryo-electron tomography data processing tasks. The toolkit includes utilities for CTF fitting on tilt series, dose correction, coordinate transformations, particle filtering, and format conversions between different software packages including emClarity, IMOD, and Warp. It also provides visualization tools for particle editing and placeback operations for structural analysis in tomographic reconstructions.

(ISOtropic reconstructioN of Electron Tomography) a tool that trains deep convolutional neural networks to reconstruct meaningful contents in the missing wedge for electron tomography, and to increase signal-to-noise ratio, using the information learned from the original tomogram.

a program that generates publication-quality protein secondary structure diagrams from three-dimensional protein structures. To depict relationships between secondary structure and other protein features, diagrams can be colored by conservation score, B-factor, or custom scoring.

a pipeline for particle detection in cryo-electron microscopy images using convolutional neural networks trained from positive and unlabeled examples. Topaz includes methods for micrograph denoising using deep denoising models.

a Python package and simple command-line program to automatically fit high-resolution atomic structures in cryo-EM densities.

a quality measure for protein, nucleic acid, and small molecule docking models that provides a single continuous scoring metric. The tool evaluates docking poses by computing interface RMSD, ligand RMSD, fraction of native contacts, and an overall DockQ score with interpretable quality thresholds.

a pipeline for particle detection in cryo-electron microscopy images using convolutional neural networks trained from positive and unlabeled examples. Topaz includes methods for micrograph denoising using deep denoising models.

a Python package that streamlines protein-protein interaction screens and high-throughput modelling of higher-order oligomers using AlphaFold-Multimer.

a user friendly and accurate binder design pipeline.

a tool that utilizes deep learning to perform volumetric electron microscopy image segmentations, both semantic and instance segmentation.