Sep 15 2024
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ColabDesign
a tool that makes protein design accessible through Jupyter notebooks by using advanced protein structure prediction models like AlphaFold and TrRosetta for designing novel proteins with targeted structures.
Updated versions:
1.1.2 | Linux 64
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Sep 13 2024
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Spyder
is a powerful scientific environment written in Python, for Python, and designed by and for scientists, engineers and data analysts.
Updated versions:
4.1.3 | OS X INTEL
5.3.2 | Linux 64
4.1.3 | Linux 64
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Sep 13 2024
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MDAnalysis
an object-oriented Python library to analyze trajectories from molecular dynamics (MD) simulations in many popular formats. It can write most of these formats, too, together with atom selections suitable for visualization or native analysis tools.
Updated versions:
2.4.2 | Linux 64
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Sep 11 2024
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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:
1.8 | OS X INTEL
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Sep 11 2024
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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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Sep 10 2024
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Glow
Glow is a versatile markdown tool offering both a text-based user interface (TUI) for interactive browsing and a command-line interface (CLI) for direct manipulation of markdown content.
Updated versions:
2.0 | OS X INTEL
2.0 | Linux 64
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Sep 10 2024
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Protkit
a Python library for structural bioinformatics, protein engineering, and machine learning. It offers tools for file handling, database access, protein representation, structure analysis, property calculation, and geometric operations.
Updated versions:
0.3.0 | Linux 64
0.3.0 | OS X INTEL
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Sep 10 2024
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2dx
a package (consisting of a suite of five programs: 2dx_manager, 2dx_image, 2dx_diffraction, 2dx_merger and 2dx_logbrowser) for user-friendly image processing of 2D crystals.
Updated versions:
3.4.2 | Linux 64
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Sep 10 2024
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Fourier3D
Updated versions:
centos_7 | Linux 64
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Sep 09 2024
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SBGrid Installer
an 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:
2.11.8 | Linux 64
2.11.8 | OS X INTEL
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Sep 08 2024
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CombFold
a pipeline that predicts the structure of large protein complexes starting from the sequences of chains in the complex, accommodating up to 18,000 amino acids and 32 subunits.
Updated versions:
20240311 | Linux 64
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Sep 06 2024
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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:
5.0-beta3_cu12.2_20240827 | Linux 64
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Sep 06 2024
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Fourier3D
Updated versions:
72a9edf | Linux 64
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Sep 06 2024
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CryoID
a graphical user interface for identification of proteins from cryo-EM maps.
Updated versions:
1.0 | Linux 64
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Sep 06 2024
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BLAST+
a suite of BLAST (Basic Local Alignment Search Tool) tools that utilizes the NCBI C++ Toolkit with a number of performance and feature improvements over the legacy BLAST applications.
Updated versions:
2.6.0 | Linux 64
2.6.0 | OS X INTEL
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Sep 05 2024
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pytom-match-pick
a GPU accelerated python module to significantly improve the speed and sensitivity using template matching to detect macromolecules from tomograms.
Updated versions:
0.7.2 | Linux 64
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Sep 04 2024
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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:
5.0-beta3_cu11.8_20240827 | Linux 64
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Sep 03 2024
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autoPROC
a tool that combines third-party processing programs with new tools for automated data processing of single-sweep, multi-sweep and multi-crystal X-ray diffraction data.
Updated versions:
20240710 | OS X INTEL
20240710 | Linux 64
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