Software Updates

PyEM

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

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.

servalcat

a structure refinement and validation for crystallography and single particle analysis.

AlphaFold

an implementation of the inference pipeline of AlphaFold using a completely new model that was entered in CASP14.

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.

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.

calc_level_chimeraX

is a ChimeraX plugin to predict and visualize isosurface levels for 3D density maps. This tool is based on a 3D-CNN initially developed to predict the isosurface levels of 3D density maps, as required by SIREn. More details about the 3D-CNN and SIREn can be found here.

Slabify

is a command-line tool designed for the automatic segmentation of lamella slabs in cryo-electron tomography (cryo-ET) volumes. It utilizes local variance analysis to identify significant density regions and offers multiple operational modes, including robust plane fitting and manual boundary definition. This tool is particularly useful for enhancing particle picking and optimizing template matching in cryo-ET data processing.

ConSurf

is a bioinformatics tool designed for estimating the evolutionary conservation of amino and nucleic acid positions in protein, DNA, and RNA molecules. It leverages phylogenetic relationships among homologous sequences to assess conservation, providing insights into structural and functional importance. ConSurf employs advanced computational methods, including empirical Bayesian and maximum likelihood approaches, to deliver accurate evolutionary rate estimations.

DeepRank-GNN-esm

a graph neural network framework for scoring protein-protein interfaces that incorporates ESM-2 language model embeddings. The tool provides both a command-line interface for direct complex scoring and a Python framework for custom applications, generating predictions of interface quality (fnat values) from PDB structures. It includes pre-trained models and supports both CPU and GPU environments for analyzing protein-protein binding interfaces.

cryomaskr

is a desktop application that provides WYSIWYG mask generation for cryo-electron microscopy data analysis. It offers an intuitive graphical interface with real-time visual feedback, eliminating the need for complex command-line operations and iterative scripting cycles. The tool integrates with standard cryoEM file formats, and includes advanced masking capabilities for complex structures and membrane proteins.

Foundry

is a unified framework for protein design that provides tooling and infrastructure for using and training models including RFdiffusion3 (all-atom generative design), RosettaFold3 (structure prediction), and ProteinMPNN/LigandMPNN (inverse folding).

OpenFold

a trainable, memory-efficient, and GPU-friendly PyTorch reproduction of DeepMind's AlphaFold 2.

SRA Toolkit

(Sequence Read Archive Toolkit) a collection of tools and libraries for using data in the INSDC Sequence Read Archives.

BioXTAS RAW

a program for analysis of SAXS data that enables creation of 1D scattering profiles from 2D detector images, standard data operations such as averaging and subtraction, analysis of radius of gyration (Rg) and molecular weight, and advanced processing using GNOM, DAMMIF, and AMBIMETER. It also allows easy processing of inline SEC-SAXS data.

SRA Toolkit

(Sequence Read Archive Toolkit) a collection of tools and libraries for using data in the INSDC Sequence Read Archives.

GROMACS

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

Curves+

a complete rewrite of the Curves approach for analyzing the structure of nucleic acids. Included are the helper programs Canal, Cdif and Sumr.

ImmuneBuilder

is a high-performance deep learning framework developed by the Oxford Protein Informatics Group (OPIG) specifically for predicting the 3D structures of immune receptor proteins.

By specializing in antibodies, nanobodies, and T-cell receptors (TCRs), it achieves state-of-the-art accuracy while delivering results over 100 times faster than general-purpose models like AlphaFold2.

OpenFreeEnergy

is a Python package for executing alchemical free energy calculations.

LASErMPNN

is an all-atom ligand-conditioned protein sequence design and sidechain packing model that accounts for the presence of small molecules, including hydrogens. It utilizes a ligand-conditioned Message Passing Neural Network architecture to design sequences for specific binding sites and can perform both de novo design and sidechain repacking. The tool is trained on protonated structures to ensure accurate physical modeling of protein-ligand interactions.

DSSR

(Dissecting the Spatial Structure of RNA) a software tool for dissecting the spatial structure of RNA.

magCalEM

Accurate magnification determination for cryoEM. Determining the correct magnified pixel size of single-particle cryoEM micrographs is necessary to maximise resolution and enable accurate model building. We provide a simple python program for determining the absolute magnification in an electron cryomicroscope to a precision of better than 0.5%. The program uses the atomic lattice spacings of crystals of thin and readily available test specimens, such as gold, as an absolute reference to determine magnification for both room temperature and cryogenic imaging. This magnification calibration method provides a definitive reference quantity for data analysis and processing, simplifies the combination of multiple datasets from different microscopes and detectors, and improves the accuracy with which the contrast transfer function of the microscope can be determined.

TomoTwin-cryoet

a deep metric learning based particle picking procedure for cryo-ET

ModelAngelo

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

MemBrain-Seg

a tool for membrane segmentation in 3D for cryo-electron tomography (cryo-ET).

RFdiffusion2

is an atom-level enzyme active site scaffolding tool that generates protein backbones conditioned on atomic motifs and small molecules. The software supports enzyme design from atomic motifs with unknown sequence positions, small-molecule binder design with RASA conditioning, and includes integration with LigandMPNN for sequence fitting and Chai1 for structure validation. It provides both indexed backbone and unindexed atomized region outputs with optional idealization steps for enhanced structural quality.

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.

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.

Dynamo

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

AlphaFold

an implementation of the inference pipeline of AlphaFold using a completely new model that was entered in CASP14.

RELION composite masks

a RELION 4 and 5 with support for composite masks

crYOLO

a automated particle picking software based on the deep learning object detection system 'You Only Look Once' (YOLO). CrYOLO is available as a standalone program under http://sphire.mpg.de/ and is part of the image processing workflow in SPHIRE.

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.

IMP

(Integrative Modeling Platform) a program designed to allow mixing and matching of existing modeling components as well as the easy addition of new functionality.

DeepRank-GNN-esm

a graph neural network framework for scoring protein-protein interfaces that incorporates ESM-2 language model embeddings. The tool provides both a command-line interface for direct complex scoring and a Python framework for custom applications, generating predictions of interface quality (fnat values) from PDB structures. It includes pre-trained models and supports both CPU and GPU environments for analyzing protein-protein binding interfaces.

VirtualIce

a feature-rich half-synthetic cryoEM micrograph generator that uses buffer cryoEM micrographs with junk and carbon masked out as real background.

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.

Tardis

a neural network-based segmentation tool that automates the analysis of cytoskeletal structures in electron microscopy data accurately distinguishing individual filaments and membranes in complex cellular environments.

smap

a tool for detecting unlabeled macromolecules in 2D Cryo-EM images of cells that uses high-resolution template matching.

RDKit

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

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.

NMRPipe

a set of comprehensive facilities for Fourier processing of spectra in one to four dimensions, as well as a variety of facilities for spectral display and analysis. This is the official NMRScience version of NMRPipe.

Dynamo

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

NMRFx Structure

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

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.

BindCraft

a user friendly and accurate binder design pipeline.

GROMACS

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

Icecream

a self-supervised framework for cryo-ET reconstruction that integrates equivariance principles from modern imaging theory into a deep-learning architecture.

PowerFit

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

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.

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.

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.

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.

ChemEX

an analysis program for chemical exchange detected by NMR.

ThermoMPNN-D

is a Siamese neural network designed to predict stability changes from protein double point mutations. The tool extends ThermoMPNN and ProteinMPNN, offering three prediction modes: single mutant, additive double mutant (which sums individual contributions), and epistatic double mutant (which captures epistatic interactions between mutations). It provides fast inference through batched predictions and includes tools for systematic analysis of all possible single or double mutants in a protein structure, outputting mutation and ΔΔG values.

ThermoMPNN

is a graph neural network (GNN) designed to predict changes in stability for protein point mutants using transfer learning. This tool is particularly useful for researchers in structural biology and bioinformatics, providing insights into protein stability alterations due to mutations. It supports customizable output locations for inference, enhancing usability in various computational environments.

anvi'o

an open-source, community-driven analysis and visualization platform for ‘omics data. Its interactive interface facilitates the management of metagenomic contigs and associated data for automatic or human-guided identification of genome bins and their curation.

RDKit

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

Volume_Seg_Tool

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

RDKit

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