Aug 31 2022
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AlphaPulldown
a Python package that streamlines protein-protein interaction screens and high-throughput modelling of higher-order oligomers using AlphaFold-Multimer.
Updated versions:
0.21.5 | Linux 64
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Aug 22 2022
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RStudio
an integrated development environment (IDE) for R that includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management.
Updated versions:
2022.02.3 | Linux 64
2022.02.3 | OS X INTEL
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Aug 19 2022
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IsoNet
(ISOtropic reconstructioN of Electron Tomography) trains deep convolutional neural networks to reconstruct meaningful contents in the missing wedge for electron tomography, and to increase signal-to-noise ratio, using the information learned from the original tomogram.
Updated versions:
0.2_cu10.2 | Linux 64
0.2 | Linux 64
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Aug 19 2022
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SAMtools
(Sequence Alignment/Map) a generic format for storing large nucleotide sequence alignments that provides various utilities for manipulating alignments, including sorting, merging, indexing and generating alignments in a per-position format.
Updated versions:
1.16 | Linux 64
1.16 | OS X INTEL
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Aug 17 2022
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xds_gsk
XDS licensed for GSK use
Updated versions:
20220110 | OS X INTEL
20220110 | Linux 64
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Aug 16 2022
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Surface Morphometrics Pipeline
a pipeline of tools to generate robust open mesh surfaces from voxel segmentations of biological membranes using the Screened Poisson algorithm and calculate morphological features including curvature and membrane-membrane distance using pycurv's vector voting framework with tools to convert these morphological quantities into morphometric insights.
Updated versions:
0.2 | Linux 64
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Aug 15 2022
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MemBrain
a pipeline for the automated detection of membrane-bound proteins in cryo-electron tomograms. It utilizes the geometry of a pre-segmented membrane to reduce the complexity of the detection task. As a result, MemBrain only requires a small amount of annotated data (even one single annotated membrane can be enough!) and can generalize well to unseen tomograms and membranes.
Updated versions:
767b477 | Linux 64
767b477 | OS X INTEL
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Aug 11 2022
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R-pkgs-SBGrid
contains optional R pkgs
Updated versions:
r4.1-latest | Linux 64
r4.1-20220810 | Linux 64
r4.1-latest | OS X INTEL
r4.1-20220810 | OS X INTEL
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Aug 10 2022
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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:
2022-3 | Linux 64
2022-3 | OS X INTEL
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Aug 09 2022
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cryoCARE
PIP package memory efficient implementation of cryoCARE (Content-Aware Image Restoration for Cryo-Transmission Electron Microscopy Data), is a restoration method that dramatically increases contrast in cryo-TEM images, improving the interpretability of the acquired data.
Updated versions:
0.1.1 | Linux 64
0.1.1 | OS X INTEL
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Aug 03 2022
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PyMOL
widely used molecular visualization package developed by Warren DeLano, now maintained by Schödinger, LLC. This installation includes official incentive builds of PyMOL.
Updated versions:
2.5.3_386 | Linux 64
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