Dec 24 2023
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MemBrain-Seg
a tool for membrane segmentation in 3D for cryo-electron tomography (cryo-ET).
Updated versions:
e28baac | Linux 64
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Dec 21 2023
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Tomo3D
a package for fast tomographic reconstruction on multicore computers. Full resolution tomograms are generated at high speed on standard computers with no special system requirements.
Updated versions:
2.2 | Linux 64
2.2 | OS X INTEL
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Dec 19 2023
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TomoTwin-cryoet
a deep metric learning based particle picking procedure for cryo-ET
Updated versions:
0.6.1a | Linux 64
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Dec 19 2023
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MemBrain-Seg
a tool for membrane segmentation in 3D for cryo-electron tomography (cryo-ET).
Updated versions:
d76e97e | Linux 64
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Dec 17 2023
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ATSAS
a program suite for small-angle scattering (SAXS) data analysis from biological macromolecules.
Updated versions:
3.2.1 | Linux 64
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Dec 15 2023
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PDB_REDO
a program that refines any structural model you are working on, by optimising REFMAC refinement and by partial model rebuilding. The process is fully automated so you only need to provide an initial structure model and your reflection data.
Updated versions:
6.0 | OS X INTEL
6.0 | Linux 64
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Dec 15 2023
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ChimeraX
a tool of the next-generation molecular visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera. Compared to Chimera, ChimeraX has improved graphics (e.g. interactive ambient shadows); faster handling of large structures (millions of atoms); and a more modern, single-window user interface.
Updated versions:
20230908 | OS X INTEL
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Dec 14 2023
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crYOLO
a novel automated particle picking software based on the deep learning object detection system 'You Only Look Once' (YOLO). CrYOLO is available as a standalone program under http://sphire.mpg.de/ and is part of the image processing workflow in SPHIRE.
Updated versions:
1.9.3_scipion | Linux 64
1.9.7 | Linux 64
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Dec 14 2023
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Scipion
an image processing framework to obtain 3D models of macromolecular complexes using 3D EM that allows you to execute workflows combining different software tools, while taking care of formats and conversions.
Updated versions:
20230901 | Linux 64
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Dec 14 2023
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cisTEM
(Computational Imaging System for Transmission Electron Microscopy) a program that processes cryo-EM images of macromolecular complexes and obtains high-resolution 3D reconstructions with tools to process image data including movies, micrographs and stacks of single-particle images, implementing a complete “pipeline” of processing steps to obtain high-resolution single-particle reconstructions.
Updated versions:
2.0.0-alpha-183-e549844 | Linux 64
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Dec 13 2023
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emClarity
(enhanced macromolecular classification and alignment for high-resolution in situ tomography) a GPU-accelerated image processing software for high-resolution cryo-electron tomography and subtomogram averaging and classification.
Updated versions:
1.6.1 | Linux 64
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Dec 12 2023
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GCTFFind
a tool that robustly estimates the contrast transfer function (CTF) of cryoET tilt series and cryoEM micrographs, essential information needed for cryoET subtomogram averaging and cryoEM single-particle reconstruction.
Updated versions:
1.0.0 | Linux 64
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Dec 08 2023
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RxDock
a fast, versatile, and open-source program for docking ligands to proteins and nucleic acids.
Updated versions:
2013.1.0_b93747f3 | OS X INTEL
2013.1.0_b93747f3 | Linux 64
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Dec 07 2023
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Chimera
a highly extensible, interactive molecular graphics 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. It is often a tool of choice for rendering EM volumes.
Updated versions:
1.17.1_sig | OS X INTEL
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Dec 06 2023
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NMRPipe
a set of comprehensive facilities for Fourier processing of spectra in one to four dimensions, as well as a variety of facilities for spectral display and analysis. This is the official NMRScience version of NMRPipe.
Updated versions:
20230523 | OS X INTEL
20230523 | Linux 64
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Dec 06 2023
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topaz-filament
a program with added support for filament start-end coordinate picking (new options -f, -fp and -fl in the extract command extract.py) in Topaz, for subsequent helical reconstruction in RELION.
Updated versions:
20220325 | Linux 64
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Dec 06 2023
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NAMD
a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.
Updated versions:
3.0b5-universal-multicore | OS X INTEL
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Dec 05 2023
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CNIO RELION Tools
a collection of scripts for cryoEM data collection and analysis
Updated versions:
8f5dac5 | OS X INTEL
8f5dac5 | Linux 64
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Dec 04 2023
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R
a free software environment for statistical computing and graphics.
Updated versions:
4.2.1 | OS X INTEL
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Dec 04 2023
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PyTOM
a tool that unifies standard tomogram processing steps in a single python-based toolbox. For subtomogram averaging, we implemented an adaptive adjustment of scoring and sampling that clearly improves the resolution of averages compared to static strategies.
Updated versions:
1.0a | Linux 64
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Dec 01 2023
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BCFtools
a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.
Updated versions:
1.17 | OS X INTEL
1.17 | Linux 64
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