Software Updates

R

a free software environment for statistical computing and graphics.

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.

ModelAngelo

an automatic atomic model building program for cryo-EM maps.

RELION

(REgularised LIkelihood OptimisatioN) a stand-alone computer program for Maximum A Posteriori (MAP) refinement of (multiple) 3D reconstructions or 2D class averages in cryo-electron microscopy.

PowerFit

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

CryoZeta

CryoZeta is a de novo macromolecular structure modeling tool that integrates cryo-EM density information with a diffusion-model-based structure prediction pipeline.

ColabFold

an easy-to-use Notebook based environment for fast and convenient protein structure predictions.

autoPROC

a tool that combines third-party processing programs with new tools for automated data processing of single-sweep, multi-sweep and multi-crystal X-ray diffraction data.

TOMOMAN

a MATLAB package for managing the various preprocessing steps for taking raw data to reconstructed tomograms. TOMOMAN mainly acts as a set of wrapper scripts for external packages, managing the input and outputs of each external module to form a cohesive pipeline.

CryoROLE

is a python package designed to analyze the particle distribution of the relative orientation between two independently refined domains of a biological complex. The landscape is represented in angular (real) space.

MotionCor3

a multi-GPU program that corrects beam-induced sample motion on dose fractionated movie stacks. It implements a robust iterative alignment algorithm that delivers precise measurement and correction of both global and non-uniform local motions at single pixel level across the whole frame, suitable for both single-particle and tomographic images.

AlphaPulldown

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

AlphaFold3

predicts 3D molecular structures and their interactions. It generalizes the original "protein‑only" AlphaFold into a model for whole biomolecular complexes, including proteins, DNA, RNA, and ligands (small molecules).

MassiveFold

a tool designed to expand structure prediction sampling by optimizing the parallelization of AlphaFold-based predictions across GPU clusters.

RECOVAR

a software tool for analyzing different conformations in heterogeneous cryo-EM and cryo-ET datasets. RECOVAR can reconstruct high-resolution volumes, estimate conformational density and low free-energy motions, and automatically identify subsets of images with a particular volume feature.

EMReady2

is a fully automated method for improving cryo-EM and cryo-ET maps by efficiently integrating local quality-aware deep learning with Mamba.

SASSIE

a program suite used to create atomistic models of molecular systems and to compare scattering data from these models directly to experimental data.

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).

STOPGAP

a subtomogram averaging workflow written in MATLAB for performing a number of subtomogram averaging tasks including template matching, high-resolution alignment and averaging, and classification.

DeepDeWedge

a tool used for the implementation of a deep learning method for simultaneous denoising and missing wedge reconstruction in cryogenic electron tomography

BoltzGen

is a deep learning-based tool for designing protein and peptide binders against target proteins or small molecules.

BUSTER

a software system containing crystallographic structure refinement using Bayesian statistical methods (BUSTER), ligand fitting (rhofit) and a fully automated pipeline (Pipedream) to drive a structure based fragment/ligand screening pathway.

Global Phasing Suite

a program that combines installation of autoPROC, BUSTER, and SHARP available to Global Phasing consortium members.

Dynamo

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

ChemEX

an analysis program for chemical exchange detected by NMR.

RDKit

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

PyMOL

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

EPicker

is a standalone software for particle picking in cryo-EM. It is implemented based on CenterNet, an open-source deep learning detection framework. Trained and well tested on datasets containing heterogenous particles, EPicker is able to pick particles, vesicles and fibers effectively.

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.