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 If you see a package or project here that is no longer maintained or is not a good fit, please submit a pull request to improve this file.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!

• Guides
  • Official Guides
  • Third party Guides
• Softwares
• Technologies
• Computational Problems
• Validation Metrics
• DataBases
• Active Groups

An awesome list of CryoEM related guides.

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• 3 Mins Introduction of CryoEM - 3 Mins Introduction of CryoEM for beginners.
• Single-particle cryo-electron microscopy - Nature Method Review.
• CryoEM Course
• CryoEM 101
• MRC lab CryoEM

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• EMAN2 Video Tutorials

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• UCSF Chimera - An interactive visualization and analysis of structures.

• 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)
  • Nature Protocol Paper - Resolving macromolecular structures from electron cryo-tomography data using subtomogram averaging in 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.

  • RosettaCM - High-Resolution Comparative Modeling with RosettaCM
  • RosettaES - RosettaES: a sampling strategy enabling automated interpretation of difficult cryo-EM maps(2017)

• 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.

  • Buccaneer
  • SFTOOLS

• 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

• Atomic accuracy models from 4.5 Å cryo-electron microscopy data with density-guided iterative local refinement

• cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination

  • Building proteins in a day: Efficient 3D molecular reconstruction(CVPR2015)

• 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

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• Single Particle
• Tomography
• MircoED

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• Fully Automatic

  • DeepPicker - Fully Automated Particle Picking using deep learning.
  • FindEM - CCP-EM projects, automated particle picking from electron micrographs, using Fortran
  • DeepEM - A deep learning approach to single-particle recognition in cryo-electron microscopy,Yanan Zhu, Qi Ouyang, Youdong Mao.
  • SPHIRE-crYOLO - SPHIRE-crYOLO: A fast and well-centering automated particle picker for cryo-EM.
  • PIXER - PIXER: an automated particle-selection method based on segmentation using a deep neural network.
  • A fast method for particle picking in cryo-electron micrographs based on fast R-CNN
  • Real-time cryo-EM data pre-processing with warp
  • Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs
  • DRPnet - Automated Particle Picking in Cryo-Electron Micrographs using Deep Regression.

• Semi Automatic

  • AutoPicker - Semi-automated selection of cryo-EM particles in RELION-1.3.

• Relion - A Bayesian approach to refinement of 3D reconstructions or 2D class averages.
• cryoSPARC - cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination
• AuTom - AuTom: A novel automatic platform for electron tomography reconstruction

• GAN - Generative adversarial networks as a tool to recover structural information from cryo-electron microscopy data.

• Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM - Xueming Li's work.

• 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.
• De novo protein structure determination from near-atomic-resolution cryo-EM maps
• Atomic accuracy models from 4.5 Å cryo-electron microscopy data with density-guided iterative local refinement
• EMfold - Meiler Lab, placement of helices is restricted to CryoEM density regions.
• SSE based methods.
• Backbone tracing methods.
• 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
• Book chapter, Review - Tools for Model Building and Optimization into Near-Atomic Resolution Electron Cryo-Microscopy Density Maps
• MAINMAST - from Kihara Lab, Terashi, Genki, and Daisuke Kihara. "De novo main-chain modeling for EM maps using MAINMAST." Nature communications 9.1 (2018): 1618.
• A^2-Net, A^2-Net: Molecular Structure Estimation from Cryo-EM Density Volumes, The 33rd AAAI Conference on Artificial Intelligence (AAAI) (2019)
• Map_to_model,biorxiv Version, A fully automatic method yielding initial models from high-resolution electron cryo-microscopy

• EMAN2.2 - Convolutional neural networks for automated annotation of cellular cryo-electron tomograms
• Convolutional Neural Networks for　Automated Annotation of Cellular CryoElectron　Tomograms
• Deep learning based subdivision approach for large scale macromolecules structure recovery from electron cryo tomograms
• pytom Tutorial

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• RMSD - Root Mean Square Deviation
• FSC - Fourier shell correlation.
• B-factor - A measure of (local) mobility in the (macro)molecule.
• GDT-HA - The percentage of correctly aligned residues in the 5 Å LGA sequence-independent superposition of the model and experimental structure of the target.
• GDT-TS
• AL0

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• EMDB - The Electron Microscopy Data Bank (EMDB)
• EMPIAR - EMPIAR, the Electron Microscopy Pilot Image Archive, is a public resource for raw, 2D electron microscopy images.
  • EMPIAR: a public archive for raw electron microscopy image data
• PDB - Protein Data Bank
• PDBe - Protein Data Bank in Europe
• PDBj - Protein Data Bank Japan
• wwPDB - WorldWide Protein Data Bank
• sbkb - Structural Biology Knowledgebase, A comprehensive resource for developments both in structural genomics and structural biology.

• MRC - MRC Laboratory of Molecular Biology
  • Richard Henderson - Richard Henderson Lab (The Nobel Prize in Chemistry 2017)
  • Scheres - Relion Author.
• Joachim Frank - Franklin Lab (The Nobel Prize in Chemistry 2017)
• Bob Glaeser - Single-particle electron cryo-microscopy.
• Yifan Cheng - TRPA1.
• Yigong Shi - Spliceosome, pre-mRNA splicing, γ-Secretase, Apoptosis.
• Eva Nogales - CryoEM.
• David Baker - Rosetta.
• Frank DiMaio - CryoEM model building.
• Xueming Li - Motion Correction.
• Hong-wei Wang
• Marcus Brubakero - CryoEM 3D Molecular Reconstruction, Machine Learning, CVPR 2015.
• Meiler Lab - Computational Chemical and Structural Biology, EMfold.
• Sriram Subramaniam
• Michael Cianfrocco Lab
• Kihara Lab

3D-EM Laboratories

• EMAN2
• Resource from Meiler Lab - Rosetta Tutorials, Teaching Resources, etc.

• Software Tools For Molecular Microscopy
• 3D-EM Laboratories

• More usefull tools should be added in.
• SSE prediction based model building methods.
• Prepare for Tomograpy methods.