Software Updates

PowerFit

a Python package and simple command-line program to automatically fit high-resolution atomic structures in cryo-EM densities.

AlphaPulldown

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

OpenFold3

is a biomolecular structure prediction model aiming to be a bitwise reproduction of DeepMind's AlphaFold3, developed by the AlQuraishi Lab at Columbia University and the OpenFold consortium. It supports structure prediction of standard and non-canonical protein, RNA, and DNA chains, and small molecules, with pipelines for generating MSAs using ColabFold server or JackHMMER/hhblits following the AlphaFold3 protocol. The tool includes kernel acceleration through cuEquivariance and DeepSpeed4Science kernels, multi-query job support with distributed predictions across multiple GPUs, and performs competitively with state-of-the-art open source biomolecular structure prediction models.

Warp

a set of tools for cryo-EM and cryo-ET data processing including, among other tools: Warp, M, WarpTools, MTools, MCore, and Noise2Map.

Schrodinger

a suite of tools for drug discovery

cryoCAT

an open source, GPL-3.0+ licensed library providing contextual analysis tools for cryo electron tomography and subtomogram averaging.

Scipion

Scipion is an open-source cryo-EM workflow platform that supports complete SPA and Tomography pipelines, from raw movies or tilt-series movies to final post-processed maps. It combines Xmipp algorithms with leading cryo-EM software. It can complement or provide an alternative to full-pipeline packages such as RELION and cryoSPARC, while taking care of formats and conversions in a completely transparent way for the user.

R

a free software environment for statistical computing and graphics.

Open Force Field Toolkit

a Python toolkit for the development and application of modern molecular mechanics force fields, leveraging direct chemical perception and rigorous statistical parameterization methods.

AlphaPulldown

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

OpenMM

a high performance toolkit for molecular simulation that can be used either as a stand-alone application for running simulations or as a library you call from your own code.

Open Force Field Toolkit

a Python toolkit for the development and application of modern molecular mechanics force fields, leveraging direct chemical perception and rigorous statistical parameterization methods.

OpenMM

a high performance toolkit for molecular simulation that can be used either as a stand-alone application for running simulations or as a library you call from your own code.

Open Force Field Toolkit

a Python toolkit for the development and application of modern molecular mechanics force fields, leveraging direct chemical perception and rigorous statistical parameterization methods.

pytom-match-pick

a GPU accelerated python module to significantly improve the speed and sensitivity using template matching to detect macromolecules from tomograms.

miss-alignment

is a GPU-based tool for improving cryo-ET tilt-series alignments, designed to run from an initial eTomo/WarpTools patch-tracking alignment. It provides a command-line workflow for training and reconstruction across one or more GPUs, with guidance for WarpTools and single-node SLURM use.

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.

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.

OCTOPI

is a deep-learning framework for automated 3D particle picking in cryo-electron tomography, with tools for training and running 3D U-Net models and automatically exploring model configurations.

GROMACS

a versatile package that performs molecular dynamics of proteins, lipids and nucleic acids.

AmberTools

a suite of programs that allows users to carry out molecular dynamics simulations, particularly on biomolecules. The suite can be used to carry out complete (non-periodic) molecular dynamics simulations (using NAB) with either explicit water or generalized Born solvent models. The independently developed packages work well by themselves, and with Amber itself.

Coot

(Crystallographic Object-Oriented Toolkit) an application that supports model building and real space refinement. This application interfaces with refmac, Phenix, and several other applications. Coot was recognized as the best structural biology application in 2008 by SBGrid.

OpenFold3

is a biomolecular structure prediction model aiming to be a bitwise reproduction of DeepMind's AlphaFold3, developed by the AlQuraishi Lab at Columbia University and the OpenFold consortium. It supports structure prediction of standard and non-canonical protein, RNA, and DNA chains, and small molecules, with pipelines for generating MSAs using ColabFold server or JackHMMER/hhblits following the AlphaFold3 protocol. The tool includes kernel acceleration through cuEquivariance and DeepSpeed4Science kernels, multi-query job support with distributed predictions across multiple GPUs, and performs competitively with state-of-the-art open source biomolecular structure prediction models.

Foldtree

a snakemake workflow for making and benchmarking structure based trees using Foldseek.

R

a free software environment for statistical computing and graphics.

ICM-Browser-Pro

a high quality visualizer and annotator for three dimensional molecular structures, sequences, alignments, chemical spreadsheets and biological data.

DIALS

(Diffraction Integration for Advanced Light Sources) a software project for the analysis of crystallographic diffraction images for many new methods from shutterless, fine-sliced rotation scans to randomly-oriented snapshots of serial crystallography. It uses multiple CPU and GPU machines to increase speed and accuracy based on a comprehensive physical model.

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.

NMRFx Analyst

a tool for NMR processing, visualization and analysis that integrates code of NMRFx Processor, Structure and additional tools.

pytom-match-pick

a GPU accelerated python module to significantly improve the speed and sensitivity using template matching to detect macromolecules from tomograms.

RDKit

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

PyCoAn

a Python-based framework for analyzing electron microscopy data within a unified, Matlab-like environment. The package provides a distinctive correlation-based docking methodology that uses cross-validation to define confidence intervals for solutions.

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.

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.

XDS

(X-ray Detector Software) a software tool for processing single-crystal monochromatic diffraction data recorded by the rotation method.