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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.
RosettaES / Rosetta Enumerative Sampling
Automates, improves upon, and expedites de novo model building. RosettaES uses fragment-based sampling to enumerate a ‘pool’ of possible protein conformations that both possess physically realistic geometry and are consistent with the experimental density data. It rebuilds multiple interacting segments by independently sampling and combining, iterating the process as necessary until a set of non-clashing solutions is found. RosettaES is a part of the Rosetta Suite.
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.
ROME / Refinement and Optimization based on Machine lEarning for cryo-EM
Offers a clustering method for single-particle cryo-EM data. ROME enables efficient computation of thousands of reference-free class averages in a highly affordable fashion. It can markedly improve the quality and resolution of ab initio 3D models with angular reconstitution. This tool was evaluated using several cryoEM datasets. It shows the advantage of generative topographic mapping (GTM)-based unsupervised clustering in discerning subtle structural differences directly from 2D class averages corresponding to distinct conformations.
Provides an efficient and reliable method for reconstructing a three-dimensional density map from specimens with helical symmetry. PHOELIX was developed to provide a time-efficient and semi-automated method. The procedures which are part of PHOELIX are drawn from the original MRC helical processing suite with extensions principally developed using the SUPRIM image processing package. The package has been optimized for the processing of actomyosin filaments but has been modified and applied to other helical structures.
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.
Provides an image processing environment with a particular emphasis on transmission electron microscopy (TEM) structure determination. SPARX includes a graphical user interface that provides a complete graphical programming environment with a data/process-Xow infrastructure, an extensive library of Python scripts that perform speciWc TEM-related computational tasks, and a core library of fundamental C++ image processing functions. In addition, SPARX relies on the EMAN2 library and cctbx, the open-source computational crystallography library from PHENIX. The design of the system is such that future inclusion of other image processing libraries is a straightforward task. SPARX and all dependencies are free for academic use and available with complete source.
IMIRS / Image Management and Icosahedral Reconstruction System
Consists of a complete set of modular programs for icosahedral reconstruction organized under a graphical user interface. IMIRS provides options for user-friendly, step-by-step data processing as well as automatic reconstruction. The integration of data management with processing in IMIRS automates the tedious tasks of data management, enables data coherence, and facilitates information sharing in a distributed computer and user environment without significantly increasing the time of program execution.
Allows for individual <1 MDa particle images to be aligned without frame averaging or linear trajectories. The lm-bfgs algorithm maximizes the overall correlation of the shifted frames with the sum of the shifted frames. The optimum in this single objective function is found efficiently by making use of analytically calculated derivatives of the function. To smooth estimates of particle trajectories, rapid changes in particle positions between frames are penalized in the objective function and weighted averaging of nearby trajectories ensures local correlation in trajectories. This individual particle motion correction, in combination with weighting of Fourier components to account for increasing radiation damage in later frames, can be used to improve 3-D maps from single particle cryo-electron microscopy.
SIMPLE / Single-particle IMage Processing Linux Engine
Provides data analysis methods for single-particle cryo-electron microscopy (cryo-EM). SIMPLE addresses the problem of obtaining 3D reconstructions from 2D projections only, without using an input reference volume for approximating orientations. The SIMPLE reconstruction algorithm is tailored to asymmetrical and structurally heterogeneous single-particles. Its basis is global optimization with the use of Fourier common lines. In SIMPLE, ab initio reconstruction is feasible because the 3D in-plane alignment is approximated using reference-free 2D rotational alignment. The subsequent common lines-based search hence searches projection directions and states only. Thousands of class averages are analyzed simultaneously in a matter of hours. Novice SIMPLE users get a head start via the well documented front-end.
SPRING / Single Particle Reconstruction from Images of kNown Geometry
Provides a single-particle based helical reconstruction package for electron cryo-micrographs. SPRING has been used to determine 3D structures of a variety of highly ordered and less ordered specimens. Spring provides the entire single-particle based work-flow required for helical reconstruction including: classification, helical symmetry determination and refinement tools, high-resolution structure refinement, and multi-symmetry structure refinement.
Accelerates maximum-likelihood reconstructions. The speedup is by orders of magnitude, and the SubspaceEM algorithm produces similar quality reconstructions compared to the traditional maximum-likelihood formulation. This approach uses subspace approximations of the cryo-electron microscopy images and the structure projections, greatly reducing the number of image transformations and comparisons that are computed. Experiments using simulated and actual cryo-EM data show that speedup in overall execution time compared to traditional maximum-likelihood reconstruction reaches factors of over 300.
DeepEM / Deep Electronic Microscopy
Permits to detect “good particles” from cryo-electronic microscopy (EM) micrographs taken in a variety of situations. DeepEM is based on a convolutional neural network, a multilayered neural network with local connections. It was tested on the Keyhole Limpet Hemocyanin (KLH) dataset. The tool achieves recall and precision score about 90 per cent at the same time in the precision-recall curve plotted against a manually selected set of particle images from 32 micrographs.
MultiColorSPR / Multicolor single particle reconstruction
Permits users to achieve multi-color single particle reconstruction from single molecule localization microscopy (SMLM) datasets. MultiColorSPR creates large dual-color libraries from high-throughput SMLM datasets with channel registration, particle segmentation and particle filtering image generation. It builds ground truth models of expected fluorophore positions using geometric dimensions of the complex as obtained from SMLM.
3DEMBenchmark / 3D Electron Microscopy Benchmark
Compares several algorithms using a variety of datasets and a wide range of analysis tools. 3DEMBenchmark is also used to set open challenges aiming at obtaining the lastest and most up-to-date view of the algorithm possibilities for the different image processing tasks, the goal is to foster the development of new advanced methods in the area of image processing in Structural Biology. Additionally, 3DEMBenchmark maintains a public collection of data sets for algorithm testing.
Accelerates the process of particle selection and facilitates particle selection across multiple images. SwarmPS permits to manage large scale particle selection projects. It incorporates cross-correlation and edge detection algorithms and introduces new methods of interactive parameter determination that overcome the need for user to specify algorithm-specific parameters. The tool enables user to select large data sets of single particles of arbitrary symmetry and size from electron micrographs, rapidly.
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