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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 structure refinement and validation for crystallography and single particle analysis.

an implementation of the inference pipeline of AlphaFold using a completely new model that was entered in CASP14.

(Python-based Hierarchical Environment for INtegrated Xtallography) a software suite for the automated determination of molecular structures using X-ray crystallography and other methods.

(Collaborative Computational Project, Number 4) a collection of programs and associated data and software libraries used for macromolecular structure determination by X-ray crystallography.

is a ChimeraX plugin to predict and visualize isosurface levels for 3D density maps. This tool is based on a 3D-CNN initially developed to predict the isosurface levels of 3D density maps, as required by SIREn. More details about the 3D-CNN and SIREn can be found here.

is a command-line tool designed for the automatic segmentation of lamella slabs in cryo-electron tomography (cryo-ET) volumes. It utilizes local variance analysis to identify significant density regions and offers multiple operational modes, including robust plane fitting and manual boundary definition. This tool is particularly useful for enhancing particle picking and optimizing template matching in cryo-ET data processing.

is a bioinformatics tool designed for estimating the evolutionary conservation of amino and nucleic acid positions in protein, DNA, and RNA molecules. It leverages phylogenetic relationships among homologous sequences to assess conservation, providing insights into structural and functional importance. ConSurf employs advanced computational methods, including empirical Bayesian and maximum likelihood approaches, to deliver accurate evolutionary rate estimations.

a graph neural network framework for scoring protein-protein interfaces that incorporates ESM-2 language model embeddings. The tool provides both a command-line interface for direct complex scoring and a Python framework for custom applications, generating predictions of interface quality (fnat values) from PDB structures. It includes pre-trained models and supports both CPU and GPU environments for analyzing protein-protein binding interfaces.

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.