Software Updates

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.

Leopard-EM

Leopard-EM (Location & oriEntatiOn of PARticles found using two-Dimensional tEmplate Matching) is a python package for running two-dimensional template matching (2DTM) on cryo-EM images.

DisVis

is a Python package and command line tool to visualize and quantify the accessible interaction space of distance restrained binary biomolecular complexes.

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.

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.

Global Phasing Suite

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

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.

PXDesignBench

is a protein design evaluation suite for monomer and binder tasks that standardizes sequence generation, structure consistency assessment, and downstream metrics across tools including ProteinMPNN, ESMFold, AlphaFold2, and Protenix.

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.

PRODIGY

(PROtein binDIng enerGY prediction for Binding Affinity Prediction)- a collection of web services focused on the prediction of binding affinity in biological complexes as well as the identification of biological interfaces from crystallographic one.

protein-quest

is a Python package to search/retrieve/filter proteins and protein structures.

warpylib

Spyder

is a powerful scientific environment written in Python, for Python, and designed by and for scientists, engineers and data analysts.

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.

easymode

a collection of general pretrained networks for cellular cryoET.

Ais

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

AlphaPulldown

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

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

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.

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.

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.