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
- 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
- EMAN2 Video Tutorials
- UCSF Chimera - An interactive visualization and analysis of structures.
- UCSF ChimeraX - An interactive visualization and analysis of structures. [[code]](https://github.com/RBVI/ChimeraX)
- Relion - A Bayesian approach to refinement of 3D reconstructions or 2D class averages.
- 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.
- 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.
- 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
- 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
- [paper - tools.cloud/)
- 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](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.
- [paper
- [paper
- [paper
- [paper
- [paper
- [paper
- [paper
- [paper
- [paper
- [webpage
- Nature Protocol Paper - Resolving macromolecular structures from electron cryo-tomography data using subtomogram averaging in RELION
- [code - lmb.cam.ac.uk/pub/scheres/relion21_tutorial.pdf)
- [paper
- [paper
- [code - lmb.cam.ac.uk/pub/scheres/relion31_tutorial.pdf)
- [paper
- [paper
- [paper
- [paper
- [paper
- [webpage
- [paper
- [paper
- [paper
- [paper
- [webpage
- [paper
- [paper
- [Book chapter
- [paper
- [paper - 2-Net).
- [paper - Backbone-Prediction).
- [paper
- [paper
- [paper
- [paper
- [paper - lab/EMRinger).
- 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.
- [paper - python3+variant-shape]](https://github.com/kuixu/ResMap)
- [paper
- [paper
- [paper
- [paper
- [paper
- [paper
- [webpage
- [paper
- 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
- 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
- EMAN2
- Resource from Meiler Lab - Rosetta Tutorials, Teaching Resources, etc.
- Software Tools For Molecular Microscopy
- 
Programming Languages