Software Updates

AlphaPulldown

a Python package that streamlines protein-protein interaction screens and high-throughput modelling of higher-order oligomers using AlphaFold-Multimer.

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.

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.

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.

xds_gsk

XDS licensed for GSK use

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.

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.

R-pkgs-SBGrid

contains optional R pkgs

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.

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.

PyMOL

widely used molecular visualization package developed by Warren DeLano, now maintained by Schödinger, LLC. This installation includes official incentive builds of PyMOL.