A collaborative list of awesome CryoEM (Cryo Electron Microscopy) resources.
A collaborative list of awesome CryoEM (Electron Cryo-Microscopy) resources. Feel free to contribute!
Please take a quick look at the contribution guidelines first. If you see a package or project here that is no longer maintained or is not a good fit, please submit a pull request to improve this file. Thank you to all contributors; you rock!
An awesome list of CryoEM related guides.
UCSF Chimera - An interactive visualization and analysis of structures.
UCSF ChimeraX - An interactive visualization and analysis of structures. [code]
Relion - A Bayesian approach to refinement of 3D reconstructions or 2D class averages.
New
2.1 - Tutorial (v2.1) (The quickest way to learning RELION)COOT - A interactive visualization model building, model completion and validation.
EMAN2 - A scientific image processing software suite with a focus on CryoEM and CryoET.
PHENIX - Automated determination of molecular structures using X-ray crystallography and other methods.
Rosetta - A software suite includes algorithms for computational modeling and analysis of protein structures.
FREALIGN: high-resolution refinement of single particle structures
SIMPLE: Software for ab initio reconstruction of heterogeneous single-particles
PRIME: probabilistic initial 3D model generation for single-particle cryo-electron microscopy
SPIDER - System for Processing Image Data from Electron microscopy and Related fields.
CCP4 - Collaborative Computational Project No. 4 Software for Macromolecular X-Ray Crystallography.
ResMap - computing the local resolution of 3D density maps.
DeepPicker - Fully Automated Particle Picking using deep learning.
FindEM - CCP-EM projects, automated particle picking from electron micrographs, using Fortran
EMfold - Meiler Lab, placement of helices is restricted to CryoEM density regions.
De novo protein structure determination from near-atomic-resolution cryo-EM maps
cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination
Pathwalker - Constructing and Validating Initial Cα Models from Subnanometer Resolution Density Maps with Pathwalking, TSP
EMBuilder - EMBuilder: A Template Matching-based Automatic Model-building Program for High-resolution Cryo-Electron Microscopy Maps
Cryoem-cloud-tools: A software platform to deploy and manage cryo-EM jobs in the cloud. [paper], [papge]
Fully Automatic
Semi Automatic
Relion - A Bayesian approach to refinement of 3D reconstructions or 2D class averages. [webpage], [code]
cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nature Methods, 2017. [paper]
THUNDER: A particle-filter framework for robust cryo-EM 3D reconstruction. Nature Methods, 2018. [paper]
CryoDRGN - Reconstructing continuously heterogeneous structures from single particle cryo-EM with deep generative models. ICLR 2020(spotlight). [paper].
CryoGAN: A New Reconstruction Paradigm for Single-particle Cryo-EM Via Deep Adversarial Learning. [paper].