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

is a Python pipeline for evaluating AlphaFold2 and AlphaFold3 protein complex predictions by combining model confidence metrics such as ipTM, pTM, pLDDT, and PAE with interface-level biophysical descriptors including contacts, hydrogen bonds, salt bridges, buried area, solvation proxy, and shape complementarity.

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

is a graphical interface for quantifying membrane ultrastructure in cryo-electron tomography data. It supports generating surface meshes from segmentations, measuring membrane curvature, distances, and relative orientations, and interactively visualizing the results in 3D.

a tool for scaling data analyses in cellular cryoET using comprehensive segmentation.

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 Python pipeline for evaluating AlphaFold2 and AlphaFold3 protein complex predictions by combining model confidence metrics such as ipTM, pTM, pLDDT, and PAE with interface-level biophysical descriptors including contacts, hydrogen bonds, salt bridges, buried area, solvation proxy, and shape complementarity.

a tool that provides annotation and segmentation of cryo-ET data using convolutional neural networks.

predicts 3D molecular structures and their interactions. It generalizes the original "protein‑only" AlphaFold into a model for whole biomolecular complexes, including proteins, DNA, RNA, and ligands (small molecules).

an integrated suite of software tools for processing single particle cryoEM data, from preprocessing raw image data through building and fitting atomic models.