Mar 31 2023
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cryoDRGN
a neural network based algorithm for heterogeneous cryo-EM reconstruction. In particular, the method models a continuous distribution over 3D structures by using a neural network based representation for the volume.
Updated versions:
2.2.0 | Linux 64
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Mar 31 2023
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R
a free software environment for statistical computing and graphics.
Updated versions:
4.2.3 | OS X INTEL
4.2.3 | Linux 64
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Mar 31 2023
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ChimeraX
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:
1.3 | Linux 64
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Mar 30 2023
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SBGrid Installer
The SBGrid installation manager is the primary application for managing an SBGrid software installation. Users can choose a subset of applications for installation on their laptops or desktops or configure site installations for clusters, servers or cloud resources. This version is the command-line interface. A graphical version is available for download on the SBGrid wiki : https://sbgrid.org/wiki/client_downloads .
Updated versions:
2.9.3 | Linux 64
2.9.3 | OS X INTEL
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Mar 30 2023
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XDS
(X-ray Detector Software) a software tool for processing single-crystal monochromatic diffraction data recorded by the rotation method.
Updated versions:
20220110 | OS X INTEL
20220110 | Linux 64
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Mar 28 2023
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ModelAngelo
an automatic atomic model building program for cryo-EM maps.
Updated versions:
0.2.3 | Linux 64
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Mar 27 2023
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PEET
(Particle Estimation for Electron Tomography) a package for aligning and averaging particles in 3-D subvolumes extracted from tomograms. If PEET and IMOD are both installed, most PEET operations are available from the eTomo graphical user interface in IMOD. PEET is written in Matlab and a compiled version is distributed along with the Matlab runtime environment needed to run it.
Updated versions:
1.17.0 | Linux 64
1.15.1a | Linux 64
1.15.1a | OS X INTEL
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Mar 24 2023
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Fiji
an image processing package. It can be described as a distribution of ImageJ (and ImageJ2) together with Java, Java 3D and a lot of plugins organized into a coherent menu structure. Fiji compares to ImageJ as Ubuntu compares to Linux.
Updated versions:
2.9.0 | Linux 64
2.9.0 | OS X INTEL
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Mar 24 2023
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ImageMagick
a software suite to create, edit, compose, or convert bitmap images.
Updated versions:
7.1.1-3 | OS X INTEL
7.1.1-3 | Linux 64
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Mar 22 2023
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GROMACS
a versatile package that performs molecular dynamics of proteins, lipids and nucleic acids.
Updated versions:
2022.4_cu11.5.2 | Linux 64
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Mar 22 2023
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ColabFold
an easy-to-use Notebook based environment for fast and convenient protein structure predictions.
Updated versions:
1.5.2 | Linux 64
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Mar 15 2023
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OccuPy
a fast and simple python module and program to estimate local scaling of cryo-EM maps, to approximate relative occupancy and/or resolution, and optionally to equalize the map according to occupancy while suppressing solvent amplification.
Updated versions:
0.1.11 | Linux 64
0.1.11 | OS X INTEL
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Mar 14 2023
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RELION Analyse Dashboard
a webapp to analyze in detail each RELION job in a given project.
Updated versions:
22657ee | Linux 64
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Mar 13 2023
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CCP4
(Collaborative Computational Project, Number 4) a collection of programs and associated data and software libraries used for macromolecular structure determination by X-ray crystallography.
Updated versions:
8.0 | OS X INTEL
7.1.018 | OS X INTEL
7.1 | OS X INTEL
8.0.009 | OS X INTEL
7.1 | Linux 64
7.1.018 | Linux 64
8.0.009 | Linux 64
8.0 | Linux 64
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Mar 13 2023
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FreeSASA
a C library and C++ command line tool for calculating Solvent Accessible Surface Area (SASA) of biomolecules.
Updated versions:
2.1.2 | OS X INTEL
2.1.2 | Linux 64
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Mar 09 2023
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deepTools
a suite of python tools particularly developed for the efficient analysis of high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq. deepTools contains useful modules to process the mapped reads data for multiple quality checks, creating normalized coverage files in standard bedGraph and bigWig file formats, that allow comparison between different files (for example, treatment and control). Finally, using such normalized and standardized files, deepTools can create many publication-ready visualizations to identify enrichments and for functional annotations of the genome.
Updated versions:
3.5.1 | Linux 64
3.5.1 | OS X INTEL
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Mar 09 2023
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DiffDock
a state-of-the-art method for molecular docking
Updated versions:
73ef67f | Linux 64
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Mar 09 2023
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IMOD
a set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections.
Updated versions:
4.12.37 | Linux 64
4.12.37 | OS X INTEL
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Mar 09 2023
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ChimeraX
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:
20220407 | Linux 64
1.5 | Linux 64
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Mar 08 2023
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RELION
(REgularised LIkelihood OptimisatioN) a stand-alone computer program for Maximum A Posteriori (MAP) refinement of (multiple) 3D reconstructions or 2D class averages in cryo-electron microscopy.
Updated versions:
4.0.1_cu11.6 | Linux 64
4.0.1_cu10.1_legacy | Linux 64
4.0.1_m1 | OS X INTEL
4.0.1 | OS X INTEL
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Mar 08 2023
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EMBuild
an automatic model building method of multi-chain protein complexes from intermediate-resolution cryo-EM maps, integrating AlphaFold structure prediction, FFT-based global fitting, domain-based semi-flexible refinement, and graph-based iterative assembling on the main-chain probability map predicted by a deep convolutional network.
Updated versions:
1.0 | Linux 64
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Mar 08 2023
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PEET
(Particle Estimation for Electron Tomography) a package for aligning and averaging particles in 3-D subvolumes extracted from tomograms. If PEET and IMOD are both installed, most PEET operations are available from the eTomo graphical user interface in IMOD. PEET is written in Matlab and a compiled version is distributed along with the Matlab runtime environment needed to run it.
Updated versions:
1.16.0 | Linux 64
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Mar 08 2023
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EMAN2
a scientific image processing suite with a particular focus on single particle reconstruction from cryoEM images. EMAN2 is a complete refactoring of the original EMAN1 library and contains the SPARX applications.
Updated versions:
2.99 | Linux 64
2.99 | OS X INTEL
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Mar 06 2023
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Schrodinger
a suite of tools for drug discovery. The Schrodinger suite runs on Linux and Mac workstations, but due to its size, it is not included in our default installation.
Updated versions:
2022-4 | OS X INTEL
2022-4 | Linux 64
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Mar 06 2023
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OccuPy
a fast and simple python module and program to estimate local scaling of cryo-EM maps, to approximate relative occupancy and/or resolution, and optionally to equalize the map according to occupancy while suppressing solvent amplification.
Updated versions:
0.1.8 | OS X INTEL
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Mar 03 2023
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FFmpeg
a complete, cross-platform solution to record, convert and stream audio and video.
Updated versions:
5.1.2 | Linux 64
5.1.2 | OS X INTEL
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Mar 01 2023
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IGV
(Integrative Genomics Viewer) a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations.
Updated versions:
2.16.0 | Linux 64
2.16.0 | OS X INTEL
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