Awesome CryoEM

A collaborative list of awesome CryoEM (Electron Cryo-Microscopy) resources. Feel free to contribute!

Contributing

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 If you see a package or project here that is no longer maintained or is not a good fit, please submit a pull request to improve this file.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

Contents

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

Guides

An awesome list of CryoEM related guides.

Official 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

Third party Guides

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• EMAN2 Video Tutorials

Methods and Softwares

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• 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)
  • 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.

• 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

• Cryoem-cloud-tools: A software platform to deploy and manage cryo-EM jobs in the cloud. [paper], [papge]

Technologies

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• Single Particle
• Tomography
• MircoED

Computational Problems

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Particle Picking

• 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
  • Topaz - Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs, Nature Method Version
  • DRPnet - Automated Particle Picking in Cryo-Electron Micrographs using Deep Regression.
  • AutoCryoPicker - AutoCryoPicker: An Unsupervised Learning Approach for Fully Automated Single Particle Picking in Cryo-EM Images
  • DeepCryoPicker - DeepCryoPicker: Fully Automated Deep Neural Network for Single Protein Particle Picking in cryo-EM

• Semi Automatic

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

Pre-processing and Denoising

• GAN-Denosing - Generative adversarial networks as a tool to recover structural information from cryo-electron microscopy data. [paper].
• Warp - Real-time cryo-EM data pre-processing with Warp. [paper].
• Topaz-Denoise: general deep denoising models for cryoEM. [paper], [bioRxiv]
• DeepEMhacer: a deep learning solution for cryo-EM volume post-processing. [paper]
• TranSPHIRE: Automated and feedback-optimized on-the-fly processing for cryo-EM. [paper]
• Phenix.auto_sharpen: Automated map sharpening by maximization of detail and connectivity. [paper]
• Phenix.density_modification: Automated map sharpening by maximization of detail and connectivity. [paper]
• Deepsharpen: Deep-Learning Based Sharpening Of 3D Reconstruction Map From Cryo-Electron Microscopy. [paper]
• SuperEM: Super-Resolution Cryo-EM Maps With 3D Deep Generative Networks. [paper] [code] [webpage]

Motion Correction

• Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM, [paper].

3D Reconstruction

• Relion - A Bayesian approach to refinement of 3D reconstructions or 2D class averages. [webpage], [code]

  • Nature Protocol Paper - Resolving macromolecular structures from electron cryo-tomography data using subtomogram averaging in RELION
  • 2.1 [code], Tutorial (v2.1)
  • 3.0 - New tools for automated high-resolution cryo-EM structure determination in RELION-3. [paper]
  • externprior - Exploiting prior knowledge about biological macromolecules in cryo-EM structure determination. [paper], [code] RELION external reconstruct functionality with a convolutional neural network.
  • 3.1 [code], Tutorial (v3.1)

• 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].

Model Building

• PHENIX - Automated determination of molecular structures using X-ray crystallography and other methods. [webpage].
  • Map_to_model - A fully automatic method yielding initial models from high-resolution electron cryo-microscopy. Nature Methods, 2018. [paper], [bioRxiv].
• Rosetta - A software suite includes algorithms for computational modeling and analysis of protein structures. [webpage].
  • RosettaCM - High-Resolution Comparative Modeling with RosettaCM. [paper].
  • De novo protein structure determination from near-atomic-resolution cryo-EM maps. Nature Methods, 2015. [paper].
  • Atomic accuracy models from 4.5 Å cryo-electron microscopy data with density-guided iterative local refinement. Nature Methods, 2015. [paper].
  • RosettaES: a sampling strategy enabling automated interpretation of difficult cryo-EM maps. Nature Methods, 2017. [paper].
• ISOLDE - Ease the task of model building at low resolution. [webpage].
• EMfold - Placement of helices is restricted to CryoEM density regions. [webpage]
• Pathwalker - Constructing and Validating Initial Cα Models from Subnanometer Resolution Density Maps with Pathwalking. [paper].
• EMBuilder: A Template Matching-based Automatic Model-building Program for High-resolution Cryo-Electron Microscopy Maps. [paper].
• Tools for Model Building and Optimization into Near-Atomic Resolution Electron Cryo-Microscopy Density Maps. [Book chapter].
• MAINMAST - De novo main-chain modeling for EM maps using MAINMAST. [paper], [webpage].
• A^2-Net: Molecular Structure Estimation from Cryo-EM Density Volumes. The 33rd AAAI Conference on Artificial Intelligence (AAAI), 2019. [paper], [webpage].
• Cascaded-CNN: Deep Learning to Predict Protein Backbone Structure from High-Resolution Cryo-EM Density Maps. [paper], [code].
• DeepTracer: Predicting Backbone Atomic Structure from High Resolution Cryo-EM Density Maps of Protein Complexes. [paper], [paper2], [web service].
• MSTree - Automatic building of protein atomic models from cryo-EM density maps using residue co-evolution. [paper].
• Haruspex - Automatic annotation of Cryo-EM maps with the convolutional neural network. [paper].
• Scipion - Integration of Cryo-EM Model Building Software in Scipion, 2020. [paper], [webpage], [code].

Refinement

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• Phenix.real_space_refinement
• REFMAC
• ProSMART - reference restraints for proteins and nucleic acids
• LIBG - base-pair and parallelization restraints
• Rosetta
• EM-fit
• MDFF, molecular dynamics flexible fitting
• DireX

Structure Validation

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• Molprobity
• EMRinger: side chain–directed model and map validation for 3D cryo-electron microscopy. [paper], [code].
• 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

Other Related Research/Tools

• ResMap - computing the local resolution of 3D density maps, 2013. [paper], [code],[code-python3+variant-shape] *Automated Threshold Selection for Cryo-EM Density Maps. [paper]
• Extraction of Protein Dynamics Information Hidden in Cryo-EM Map Using Deep Learning, 2020. [paper], [code]
• MicrographCleaner: a python package for cryo-EM micrograph cleaning using deep learning, [paper] -
• Deep Learning for Validating and Estimating Resolution of Cryo-Electron Microscopy Density Maps. [paper]

Tomography

• EMAN2 - A scientific image processing software suite with a focus on CryoEM and CryoET. [webpage], [code].
  • CryoET Segmentation - Convolutional Neural Networks for Automated Annotation of Cellular CryoElectron Tomograms. [paper], [arxiv]
• Subtomogram Subdivision, Deep learning based subdivision approach for large scale macromolecules structure recovery from electron cryo tomograms. [paper]
• pytom. [webpage], [Tutorial]
• emClarity: software for high-resolution cryo-electron tomography and subtomogram averaging. [paper], [code], [wiki]

DataBases

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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.

Active Groups

• MRC.
  • Richard Henderson.
  • Scheres.
• Joachim Frank.
• Bob Glaeser.
• Yifan Cheng.
• Yigong Shi.
• Eva Nogales.
• David Baker.
• Frank DiMaio.
• Xueming Li.
• Hong-wei Wang.
• Marcus Brubakero.
• Meiler Lab.
• Sriram Subramaniam.
• Michael Cianfrocco Lab.
• Kihara Lab.
• Bonnie Berger.

3D-EM Laboratories

Workshop Docs

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

Websites

• Software Tools For Molecular Microscopy

License