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Cryo-EM Image Processing Tools

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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

• 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

Conversion

• cryoSPARC to STAR (csparc2star.py) (0.5) - Convert cryoSPARC file to STAR file for RELION using csparc2star.py from pyem software package

SPHIRE

• 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.

Model building

• 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

Cryo-electron tomography

• 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