Software Updates

Ais

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

pytom-match-pick

a GPU accelerated python module to significantly improve the speed and sensitivity using template matching to detect macromolecules from tomograms.

EMReady

a tool that improves the quality and interpretability of cryo-EM maps by local and non-local deep learning

Pom

a tool for scaling data analyses in cellular cryoET using comprehensive segmentation.

Starparser

a package implemented in Python to manipulate Relion star files including counting, modifying, plotting, and sifting the data.

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.

OpenFreeEnergy

is a Python package for executing alchemical free energy calculations.

OpenForceField Toolkit

a Python toolkit for the development and application of modern molecular mechanics force fields, leveraging direct chemical perception and rigorous statistical parameterization methods.

PowerFit

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

PolNet

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

GROMACS

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

LigPlot+

a successor to the original LIGPLOT program for automatic generation of 2D ligand-protein interaction diagrams. It is run from an intuitive java interface which allows on-screen editing of the plots via mouse click-and-drag operations.

ChemEM

a tool that utilizes information from Cryo-EM density and state-of-the-art small molecule force fields to dock small molecules into protein targets.

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.

RFdiffusion

an open source method for structure generation, with or without conditional information (a motif, target etc). It can perform a whole range of protein design challenges.

Warp

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

tomostarpy

a collection of Python scripts for manipulating Relion tomo STAR files and performing various cryo-electron tomography data processing tasks.

SSDraw

a program that generates publication-quality protein secondary structure diagrams from three-dimensional protein structures. To depict relationships between secondary structure and other protein features, diagrams can be colored by conservation score, B-factor, or custom scoring.

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.

PowerFit

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

DockQ

a quality measure for protein, nucleic acid, and small molecule docking models that provides a single continuous scoring metric. The tool evaluates docking poses by computing interface RMSD, ligand RMSD, fraction of native contacts, and an overall DockQ score with interpretable quality thresholds.

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.

AlphaPulldown

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

BindCraft

a user friendly and accurate binder design pipeline.

Volume_Seg_Tool

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

ColabDesign

a tool that makes protein design accessible through Jupyter notebooks by using advanced protein structure prediction models like AlphaFold and TrRosetta for designing novel proteins with targeted structures.

RDKit

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

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.

pytom-match-pick

a GPU accelerated python module to significantly improve the speed and sensitivity using template matching to detect macromolecules from tomograms.

PowerFit

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

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.

ARCTIC-3D

a software for data-mining and clustering of protein interface information. It allows you to retrieve all the existing interface information for your desired protein from the PDBE graph database, grouping similar interfaces in interacting surfaces.

prodigy-lig

PRODIGY-LIG (PROtein binDIng enerGY prediction - LIGands) is a structure-based method for the prediction of binding affinity in protein-small ligand (such as drugs or metabolites) complexes.

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.

HADDOCK3

a new open source and modular version of HADDOCK

HADDOCK

(High Ambiguity Driven biomolecular DOCKing) relies on an approach that makes use of biochemical and/or biophysical interaction data, such as chemical shift perturbation data resulting from NMR titration experiments, mutagenesis data or bioinformatic predictions.

AlphaBridge

a script that using the output provided by Alphafold3, provides different plots and files useful for the identification of interacting interfaces