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IsoNet2 is a deep-learning software package for simultaneous missing wedge correction, denoising, and CTF correction in cryo-electron tomography reconstructions using a deep neural network trained on information from the original tomogram(s). Compared to IsoNet1, IsoNet2 produces tomograms with higher resolution and less noise in roughly a tenth of the time. The software requires full tomograms or even/odd paired tomograms as input. Paired tomograms for Noise2Noise training can be split by either frame or tilt.

(X-ray Detector Software) a software tool for processing single-crystal monochromatic diffraction data recorded by the rotation method.

is a desktop application that provides WYSIWYG mask generation for cryo-electron microscopy data analysis. It offers an intuitive graphical interface with real-time visual feedback, eliminating the need for complex command-line operations and iterative scripting cycles. The tool integrates with standard cryoEM file formats, and includes advanced masking capabilities for complex structures and membrane proteins.

(Sequence Alignment/Map) a generic format for storing large nucleotide sequence alignments that provides various utilities for manipulating alignments, including sorting, merging, indexing and generating alignments in a per-position format.

a new open source and modular version of HADDOCK

a GPU accelerated python module to significantly improve the speed and sensitivity using template matching to detect macromolecules from tomograms.

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.

is a deep learning-based tool for designing protein and peptide binders against target proteins or small molecules.

a tool of the next-generation molecular visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera. Compared to Chimera, ChimeraX has improved graphics (e.g. interactive ambient shadows); faster handling of large structures (millions of atoms); and a more modern, single-window user interface.

(REgularised LIkelihood OptimisatioN) a stand-alone computer program for Maximum A Posteriori (MAP) refinement of (multiple) 3D reconstructions or 2D class averages in cryo-electron microscopy.