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Enables rapid, unbiased, and high-throughput structure discovery of proteins and molecular complexes from single-particle cryo-EM data. The algorithms underlying cryoSPARC enable high-resolution reconstructions of research and drug targets within minutes of collecting microscope data, and without the need for prior knowledge of the target structure. Using cryoSPARC can remove the risk of biased results, allow the discovery of unexpected structures, and speed up Cryo-electron microscopy workflow by orders of magnitude. Furthermore, the graphical user interface allows multiple users within a laboratory to have separate accounts, access the program remotely, upload and share data sets, manage experimental results, launch computational tasks, and view results streaming in real time as they are computed.
Calculates and refines three-dimensional (3D) structures of macromolecular assemblies that are calculated from images collected on an electron microscope. Frealign provides a fast and accurate projection matching algorithm, and calculates 3D reconstructions that are fully corrected for the contrast transfer function (CTF) of the microscope. Other features include refinement of microscope defocus and magnification, correction for the Ewald sphere curvature, processing of helical particles, 3D classification, and density masking. Furthermore, algorithms and run scripts were developed to take advantage of parallel computing environments to speed up processing.
cisTEM / Computational Imaging System for Transmission Electron Microscopy
Permits the treatment of cryo-electron microscopy (cryo-EM) images of macromolecular complexes. cisTEM is able to extract high-resolution 3D reconstructions form these images. It can deal with movies, micrographs and stacks of single-particle images, implementing a complete pipeline of processing steps. This tool is based on a maximum-likelihood algorithm. Users can define a combination of particle image stack, alignment parameters and a 3D reference structure.
RELION / REgularised LIkelihood OptimisatioN
Employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM). RELION is implemented as a stand-alone program, and its open-source C++ code is available for download. Application of RELION to both simulated and experimental data illustrates that reconstructions that are free from overfitting may be obtained in a highly objective manner, without compromising reconstruction quality and at acceptable computational costs.
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