Ecosyste.ms: Awesome
An open API service indexing awesome lists of open source software.
awesome-cryoem
A collaborative list of awesome CryoEM (Cryo Electron Microscopy) resources.
https://github.com/kuixu/awesome-cryoem
Last synced: 1 day ago
JSON representation
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Computational Problems
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Model Building
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- [paper - 2-Net).
- [paper - Backbone-Prediction).
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3D Reconstruction
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- [code - lmb.cam.ac.uk/pub/scheres/relion21_tutorial.pdf)
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- [code - lmb.cam.ac.uk/pub/scheres/relion31_tutorial.pdf)
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- Nature Protocol Paper - Resolving macromolecular structures from electron cryo-tomography data using subtomogram averaging in RELION
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Particle Picking
- FindEM - CCP-EM projects, automated particle picking from electron micrographs, using Fortran
- PIXER - PIXER: an automated particle-selection method based on segmentation using a deep neural network.
- 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.
- A fast method for particle picking in cryo-electron micrographs based on fast R-CNN
- Topaz - Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs, [Nature Method Version](https://www.ncbi.nlm.nih.gov/pubmed/29707703)
- 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
- AutoPicker - Semi-automated selection of cryo-EM particles in RELION-1.3.
- Topaz - Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs, [Nature Method Version](https://www.ncbi.nlm.nih.gov/pubmed/29707703)
- DeepPicker - Fully Automated Particle Picking using deep learning.
- A fast method for particle picking in cryo-electron micrographs based on fast R-CNN
- DeepEM - A deep learning approach to single-particle recognition in cryo-electron microscopy,Yanan Zhu, Qi Ouyang, Youdong Mao.
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Pre-processing and Denoising
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Motion Correction
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Structure Validation
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Refinement
- [paper - lab/EMRinger).
- [paper - lab/EMRinger).
- RMSD - Root Mean Square Deviation
- FSC - Fourier shell correlation.
- B-factor - A measure of (local) mobility in the (macro)molecule.
- [paper - lab/EMRinger).
- 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.
- [paper - lab/EMRinger).
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Other Related Research/Tools
- [paper - python3+variant-shape]](https://github.com/kuixu/ResMap)
- [paper - python3+variant-shape]](https://github.com/kuixu/ResMap)
- [paper
- [paper
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- [paper - python3+variant-shape]](https://github.com/kuixu/ResMap)
- [paper - python3+variant-shape]](https://github.com/kuixu/ResMap)
- [paper - python3+variant-shape]](https://github.com/kuixu/ResMap)
- [paper - python3+variant-shape]](https://github.com/kuixu/ResMap)
- [paper - python3+variant-shape]](https://github.com/kuixu/ResMap)
- [paper - python3+variant-shape]](https://github.com/kuixu/ResMap)
- [paper - python3+variant-shape]](https://github.com/kuixu/ResMap)
- [paper - python3+variant-shape]](https://github.com/kuixu/ResMap)
- [paper - python3+variant-shape]](https://github.com/kuixu/ResMap)
- [paper - python3+variant-shape]](https://github.com/kuixu/ResMap)
- [paper - python3+variant-shape]](https://github.com/kuixu/ResMap)
- [paper - python3+variant-shape]](https://github.com/kuixu/ResMap)
- [paper - python3+variant-shape]](https://github.com/kuixu/ResMap)
- [paper - python3+variant-shape]](https://github.com/kuixu/ResMap)
- [paper - python3+variant-shape]](https://github.com/kuixu/ResMap)
- [paper - python3+variant-shape]](https://github.com/kuixu/ResMap)
- [paper - python3+variant-shape]](https://github.com/kuixu/ResMap)
- [paper - python3+variant-shape]](https://github.com/kuixu/ResMap)
- [paper - python3+variant-shape]](https://github.com/kuixu/ResMap)
- [paper - python3+variant-shape]](https://github.com/kuixu/ResMap)
- [paper - python3+variant-shape]](https://github.com/kuixu/ResMap)
- [paper - python3+variant-shape]](https://github.com/kuixu/ResMap)
- [paper - python3+variant-shape]](https://github.com/kuixu/ResMap)
- [paper - python3+variant-shape]](https://github.com/kuixu/ResMap)
- [paper - python3+variant-shape]](https://github.com/kuixu/ResMap)
- [paper - python3+variant-shape]](https://github.com/kuixu/ResMap)
- [paper - python3+variant-shape]](https://github.com/kuixu/ResMap)
- [paper - python3+variant-shape]](https://github.com/kuixu/ResMap)
- [paper - python3+variant-shape]](https://github.com/kuixu/ResMap)
- [paper - python3+variant-shape]](https://github.com/kuixu/ResMap)
- [paper - python3+variant-shape]](https://github.com/kuixu/ResMap)
- [paper - python3+variant-shape]](https://github.com/kuixu/ResMap)
- [paper - python3+variant-shape]](https://github.com/kuixu/ResMap)
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Tomography
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Guides
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Official 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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Third party Guides
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Methods and Softwares
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Third party Guides
- 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.
- 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.
- EMfold - Meiler Lab, placement of helices is restricted to CryoEM density regions.
- [paper - tools.cloud/)
- EMBuilder - EMBuilder: A Template Matching-based Automatic Model-building Program for High-resolution Cryo-Electron Microscopy Maps
- UCSF ChimeraX - An interactive visualization and analysis of structures. [[code]](https://github.com/RBVI/ChimeraX)
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DataBases
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Tomography
- 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
- PDBe - Protein Data Bank in Europe
- PDBj - Protein Data Bank Japan
- wwPDB - WorldWide Protein Data Bank
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Active Groups
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Workshop Docs
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Tomography
- Resource from Meiler Lab - Rosetta Tutorials, Teaching Resources, etc.
- EMAN2
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Websites
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Tomography
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Categories