Software Updates

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.

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.

Ais

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

HADDOCK3

a new open source and modular version of HADDOCK

AlphaPulldown

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

PyEM

a set of Python modules and command-line utilities for electron microscopy of biological samples.

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.

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.

PowerFit

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

ChemEX

an analysis program for chemical exchange detected by NMR.

Protenix

a trainable PyTorch reproduction of AlphaFold 3.

Mosaic

is a graphical tool for analysing and modelling biological membranes from 3D structural data. It combines tomogram import, membrane segmentation and surface meshing with protein localization and geometric measurements, and can export simulation-ready membrane systems for downstream molecular modelling and GROMACS workflows.

IMOD

a set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections.

NAMD

a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.

PolNet

a Python package for generating synthetic datasets of the cellular context for Cryo-Electron Tomography.

PottsMPNN

is a protein design model for generating sequences from protein structures and predicting the energetic effects of mutations. It supports sequence optimization for stability and binding affinity, deep mutational scanning, and common ProteinMPNN-style design constraints.

ChemEX

an analysis program for chemical exchange detected by NMR.

Meteor

is a tool for computing crystallographic difference maps that specializes in robust identification of weak signals from minor populations such as bound ligands or time-resolved experimental changes.

PEET

(Particle Estimation for Electron Tomography) a package for aligning and averaging particles in 3-D subvolumes extracted from tomograms. If PEET and IMOD are both installed, most PEET operations are available from the eTomo graphical user interface in IMOD. PEET is written in Matlab and a compiled version is distributed along with the Matlab runtime environment needed to run it.

emClarity

(enhanced macromolecular classification and alignment for high-resolution in situ tomography) a GPU-accelerated image processing software for high-resolution cryo-electron tomography and subtomogram averaging and classification.

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.