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 If you see a package or project here that is no longer maintained or is not a good fit, please submit a pull request to improve this file.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.
- 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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UCSF Chimera - An interactive visualization and analysis of structures.
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Relion - A Bayesian approach to refinement of 3D reconstructions or 2D class averages.
New2.1 - 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
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COOT - A interactive visualization model building, model completion and validation.
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EMAN2 - A scientific image processing software suite with a focus on CryoEM and CryoET.
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PHENIX - Automated determination of molecular structures using X-ray crystallography and other methods.
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Rosetta - A software suite includes algorithms for computational modeling and analysis of protein structures.
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FREALIGN: high-resolution refinement of single particle structures
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SIMPLE: Software for ab initio reconstruction of heterogeneous single-particles
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PRIME: probabilistic initial 3D model generation for single-particle cryo-electron microscopy
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SPIDER - System for Processing Image Data from Electron microscopy and Related fields.
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CCP4 - Collaborative Computational Project No. 4 Software for Macromolecular X-Ray Crystallography.
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ResMap - computing the local resolution of 3D density maps.
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DeepPicker - Fully Automated Particle Picking using deep learning.
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FindEM - CCP-EM projects, automated particle picking from electron micrographs, using Fortran
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EMfold - Meiler Lab, placement of helices is restricted to CryoEM density regions.
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De novo protein structure determination from near-atomic-resolution cryo-EM maps
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cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination
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Pathwalker - Constructing and Validating Initial Cα Models from Subnanometer Resolution Density Maps with Pathwalking, TSP
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EMBuilder - EMBuilder: A Template Matching-based Automatic Model-building Program for High-resolution Cryo-Electron Microscopy Maps
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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.
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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
- 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
- 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.
- 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
- EMAN2
- Resource from Meiler Lab - Rosetta Tutorials, Teaching Resources, etc.
- More usefull tools should be added in.
- SSE prediction based model building methods.
- Prepare for Tomograpy methods.
