Cryo-EM Image Processing Tools
If there is a tool or a feature you need, please let us know.
Protein structure prediction
- AlphaFold2 (2.3.2) - Highly accurate protein structure prediction
- ColabFold (1.5.2) - Fast and convenient protein structure predictions using MMseqs2 and AlphaFold
- ESMFold (1.0.3) - Evolutionary-scale prediction of atomic level protein structure with a language model
- IgFold (0.0) - Fast and convenient protein structure predictions using IgFold
- OmegaFold (1.0.2) - High-resolution de novo Structure Prediction from Primary Sequence
- RELION 2D classification (3.1) - Calculate 2D class averages using RELION
- RELION 3D classification (3.1) - Perform 3D classification of single particles with 3D model using RELION
- RELION 3D initial model calculation (3.1) - Calculate initial 3D models using RELION
- RELION 3D refinement (3.1) - Iteratively refine 3D volume against single particles using RELION
- RELION 3D Multibody refinement (3.1) - Iteratively refine masked regions separately within a structure RELION
- RELION Postprocess (3.1) - Sharpen and filter 3D reconstruction using RELION
- cryoSPARC to STAR (csparc2star.py) (0.5) - Convert cryoSPARC file to STAR file for RELION using csparc2star.py from pyem software package
- crYOLO (1.7.6) - Automatic particle picking using crYOLO
- ISAC 2D classification (2.3.4) - Calculate 2D class averages using iterative stable alignment and classification (ISAC)
Validation and Analysis
- AlignProjections (1.0) - Align projections of PDB or MRC with class averages.
- Efficiency (cryoEF) (1.1.1) - Calculate efficiency for 3D reconstruction to determine if Euler angle coverage is evenly distributed
- DeepEMhancer (0.13) - Non-linear post-processing of cryo-EM maps for local sharpening-like post-processing and automatic masking/denoising.
- Local B-Factor Estimation (0.0) - Local computational methods to improve the interpretability and analysis of cryo-EM maps.
- LocBfactor Map Enhancement (0.0) - Local computational methods to improve the interpretability and analysis of cryo-EM maps.
- LocSpiral Map Enhancement (0.0) - Local computational methods to improve the interpretability and analysis of cryo-EM maps.
- LocOccupancy Map Analysis (0.0) - Local computational methods to improve the interpretability and analysis of cryo-EM maps.
- HHBlits (3.3.0) - HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment
- Model Angelo (1.0.1) - Automatic atomic model building program for cryo-EM maps
- IsoNet - Refine (0.2) - Isotropic Reconstruction of Electron Tomograms with Deep Learning
3D heterogeneity analysis
- cryoDRGN - Deep Reconstructing Generative Networks for cryo-EM heterogeneous reconstruction (0.3.1) - Perform structural analysis of 3D reconstructions using deep learning