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A collaborative list of awesome CryoEM (Cryo Electron Microscopy) resources.

Awesome CryoEM

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

Cryo-EM

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 If you see a package or project here that is no longer maintained or is not a good fit, please submit a pull request to improve this file.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

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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

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.
  • 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

3D-EM Laboratories

Workshop Docs

Websites

License

CC0

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Metadata

A collaborative list of awesome CryoEM (Cryo Electron Microscopy) resources.

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