Software Updates

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.

cryoTIGER

(Tilt Interpolation Generator for Enhanced Reconstruction) in cryo-electron tomographya computational workflow leveraging a deep learning-based frame interpolation to generate intermediate tilt images. By interpolating between tilt series projections, cryoTIGER improves angular sampling, leading to enhanced 3D reconstructions, more refined particle localization, and improved segmentation of cellular structures.

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.

Warp

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

PyRosetta

an interactive Python-based interface to the powerful Rosetta molecular modeling suite that enables users to design their own custom molecular modeling algorithms using Rosetta sampling methods and energy functions.

CcpNmr Analysis

a series of programs for macromolecular NMR including AnalysisAssign, AnalysisScreen, AnalysisMetabolomics and AnalysisStructure, and with version 3, the addition CcpNmr ChemBuild.

cryoDRGN-AI

a neural network-based algorithm for ab initio heterogeneous cryo-EM reconstruction.

Spring

(Single Particle Reconstruction from Images of kNown Geometry) a single-particle based helical reconstruction package for electron cryo-micrographs used to determine 3D structures of either highly ordered or less ordered specimens.

E3-CryoFold

a deep learning framework for automating the determination of three-dimensional atomic structures from high-resolution cryo-electron microscopy (Cryo-EM) density maps. It addresses the limitations of existing AI-based methods by providing an end-to-end solution that integrates training and inference into a single streamlined pipeline. E3-CryoFold combines 3D and sequence Transformers for feature extraction and employs an equivariant graph neural network to build accurate atomic structures from density maps.

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.

Topaz

a pipeline for particle detection in cryo-electron microscopy images using convolutional neural networks trained from positive and unlabeled examples. Topaz includes methods for micrograph denoising using deep denoising models.

Volume_Seg_Tool

a tool that utilizes deep learning to perform volumetric electron microscopy image segmentations, both semantic and instance segmentation.

ISOLDE

an immersive environment designed to ease the task of building high quality macromolecular models into low to medium resolution experimental maps, where the experimental information alone is insufficient to place individual atoms precisely. ISOLDE is implemented as a plugin to ChimeraX and can be conveniently installed via its built-in Tool Shed.

Napari

a Python library for n-dimensional image visualization, annotation, and analysis.

Gnuplot

a portable command-line driven graphing utility originally created to allow scientists and students to visualize mathematical functions and data interactively. It has grown to support many non-interactive uses such as web scripting. It is also used as a plotting engine by third-party applications like CCP4 and Octave.

ACPYPE

AnteChamber PYthon Parser interfacE: A tool based in Python to use Antechamber to generate topologies for chemical compounds and to interface with others python applications like CCPN and ARIA.

Scipion

an image processing framework to obtain 3D models of macromolecular complexes using 3D EM that allows you to execute workflows combining different software tools, while taking care of formats and conversions.

CryoNeRF

a computational tool for homogeneous and heterogeneous (conformational and compositional) cryo-EM reconstruction in Euclidean 3D space.

qFit

a collection of programs for modeling multi-conformer protein structures.

Volume_Seg_Tool

a tool that utilizes deep learning to perform volumetric electron microscopy image segmentations, both semantic and instance segmentation.

qFit

a collection of programs for modeling multi-conformer protein structures.

Geneious

a powerful and comprehensive suite of molecular biology and NGS analysis tools.

NMRFx Structure

a tool that can be used to generate and analyze macromolecular structures and predict chemical shifts.

NMRFx Analyst

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

CryoSTAR

a neural network based framework for recovering conformational heterogenity of protein complexes.

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.

XDS

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

Python

a general-purpose, interpreted, object oriented, high-level dynamic programming language that emphasizes code readability. Its syntax allows programmers to express concepts in fewer lines of code than in C++ or Java, thus allowing programmers to work more quickly and integrate their systems more effectively.

AlphaPulldown

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

Rosetta

a software suite for modeling macromolecular structures and for predicting and designing protein structures, protein folding mechanisms, and protein-protein interactions.

Global Phasing Suite

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

fpocket

an open source protein pocket (cavity) detection algorithm based on Voronoi tessellation. It was developed in the C programming language and is currently available as command line driven program.

MDAnalysis

an object-oriented Python library to analyze trajectories from molecular dynamics (MD) simulations in many popular formats. It can write most of these formats, too, together with atom selections suitable for visualization or native analysis tools.

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.

CCP-EM

(Collaborative Computational Project for Electron cryo-Microscopy) a software framework and resulting software suite that includes tools for project and data management along with a focus on building and refinement of atomic models into cryo-EM reconstructions. The framework allows easy access to various programs and utilities from collaborators via Python task wrappers and a user-friendly graphical user interface or a command-line interface suitable for scripting.

Boltz-1

an open-source model which predicts the 3D structure of proteins, rna, dna and small molecules; it handles modified residues, covalent ligands and glycans, as well as condition the generation on pocket residues.

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.

R

a free software environment for statistical computing and graphics.

TEMPy-ReFF

a tool that helps flexible-fitting and refinement of atomic models into cryo-EM maps.

Boltz-1

an open-source model which predicts the 3D structure of proteins, rna, dna and small molecules; it handles modified residues, covalent ligands and glycans, as well as condition the generation on pocket residues.

CryoSieve

an advanced software solution designed for particle sorting/sieving in single particle analysis (SPA) for Cryogenic Electron Microscopy (cryo-EM).

AMPLIFY

a best-in-class protein Language Model (pLM) that is orders of magnitude less expensive to train and deploy than previous models.

Schrodinger

a suite of tools for drug discovery.

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.