Computational Tools

Below is a short list of computational tools to aid in the structural analysis of cryo-EM data. For a more complete overview of the tools available for cryo-EM density map analyses see: Baker et al., Analyses of Subnanometer Resolution Cryo-EM Density Maps. Methods in Enzymology. 2010 May; 483:1-29. Link.

Image Processing:

EMAN2

EMAN2 is the successor to EMAN1. It is a broadly based greyscale scientific image processing suite with a primary focus on processing data from transmission electron microscopes. EMAN’s original purpose was performing single particle reconstructions (3-D volumetric models from 2-D cryo-EM images) at the highest possible resolution, but the suite now also offers support for single particle cryo-ET, and tools useful in many other subdisciplines such as helical reconstruction, 2-D crystallography and whole-cell tomography. EMAN2 is capable of processing very large data sets (>100,000 particle) very efficiently (up to 20x faster than EMAN1).

IMAGIC

IMAGIC is a high end environment for the analysis of images, spectra and other multi-dimensional data-sets. IMAGIC’s software package is aimed at processing (huge) data sets from (cryo-) electron microscopy, especially in the field of single particle analyses in Structural Biology.

Molecular Modeling and Visualization:

Gorgon Project:

Gorgon is an interactive molecular modeling system specifically geared towards cryo-EM and other low resolution structures of macromolecular complexes. The long term goal of the Gorgon project is to be able to address to every part of the molecular modeling pipeline starting from the initial volumetric reconstruction of the complex all the way to the final placement of each individual atom.

Chimera

UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and animations can be generated. Chimera includes complete documentation and several tutorials.

Molecular Modeling:

Modeller

MODELLER is used for homology or comparative modeling of protein three-dimensional structures. The user provides an alignment of a sequence to be modeled with known related structures and MODELLER automatically calculates a model containing all non-hydrogen atoms. MODELLER implements comparative protein structure modeling by satisfaction of spatial restraints, and can perform many additional tasks, including de novo modeling of loops in protein structures, optimization of various models of protein structure with respect to a flexibly defined objective function, multiple alignment of protein sequences and/or structures, clustering, searching of sequence databases, comparison of protein structures, etc.

Rosetta

Rosetta is the premier software suite for modeling macromolecular structures. As a flexible, multi-purpose application, it includes tools for structure prediction, design, and remodeling of proteins and nucleic acids. Since 1998, Rosetta web servers have run billions of structure prediction and protein design simulations.

Segmentation:

Segger

Segger is a tool for segmenting 3D density maps obtained using cryo-electron microscopy. It uses the watershed method, which is fast and requires very little user input. Over-segmentation is dealt with by scale-space filtering. Segger also allows the use of segmentation results to help place or fit atomic structures into density maps.

Fitting:

Situs

Situs is a program for modeling atomic resolution structures into low-resolution density maps e.g. from electron microscopy, tomography, or small angle X-ray scattering.

EMFit

Program for fitting atomic models into electron microscopy maps. Fitting criteria includes the sum of densities at atomic sites, the lack of atoms in negative or low density, the absence of atomic clashes between symmetry-related positions of the atomic structure, and the distances between identifiable features in the map and their positions on the fitted atomic structure, etc. 

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