Software Updates

Bowtie 2

an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.

Ais

a tool that provides annotation and segmentation of cryo-ET data using convolutional neural networks.

Dynamo

a software environment for subtomogram averaging of cryo-EM data.

CellProfiler

a cell image analysis software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically.

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.

CellProfiler

a cell image analysis software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically.

PHENIX

(Python-based Hierarchical Environment for INtegrated Xtallography) a software suite for the automated determination of molecular structures using X-ray crystallography and other methods.

CellProfiler

a cell image analysis software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically.

cryosparc-tools

a toolkit for interfacing with CryoSPARC.

upside2-md

Ultra-fast, coarse-grained molecular dynamics (MD)

Protenix

a trainable PyTorch reproduction of AlphaFold 3.

SBGrid Installer

IsoNet2

a deep-learning software package for simultaneous missing wedge correction, denoising, and CTF correction in cryo-electron tomography reconstructions using a deep neural network trained on information from the original tomogram(s).

mBER-open

is a protein design framework for antibody binder design that leverages structure templates and sequence conditioning in backpropagation-based design through AlphaFold-Multimer.

RDKit

a collection of cheminformatics and machine-learning software written in C++ and Python.

Foldseek

a program that enables fast and sensitive comparisons of large structure sets.

DEEPMAINMAST

a de novo modeling protocol to build an entire protein 3D model directly from near-atomic (up to about 5 Angstrom) resolution EM map.

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.