Software Updates

Icecream

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

UNIO

a program that performs automated NMR data analysis for protein 3D structure determination. It represents the result of more than a decade of innovative research performed in order to enable accurate, objective and highly automated protein structure determination by NMR.

ROCKET

is a tool for refining AlphaFold predictions using crystallographic and cryo-EM likelihood targets. It integrates with OpenFold to condition experimental structure determination on pretrained neural networks, requiring both OpenFold and Phenix installations for automatic data preprocessing and post-refinement geometry polishing.

RDKit

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

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.

Volume_Seg_Tool

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

TomoDRGN

a tool that extends the cryoDRGN framework to cryo-ET by learning heterogeneity from datasets in which each particle is sampled by multiple projection images at different stage tilt angles.

Fiji

an image processing package. It can be described as a distribution of ImageJ (and ImageJ2) together with Java, Java 3D and a lot of plugins organized into a coherent menu structure. Fiji compares to ImageJ as Ubuntu compares to Linux.

Warp

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

BCFtools

a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.

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.

SAMtools

(Sequence Alignment/Map) a generic format for storing large nucleotide sequence alignments that provides various utilities for manipulating alignments, including sorting, merging, indexing and generating alignments in a per-position format.

Pom

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

Chimera

a highly extensible, interactive molecular graphics program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. It is often a tool of choice for rendering EM volumes.

UNIO

a program that performs automated NMR data analysis for protein 3D structure determination. It represents the result of more than a decade of innovative research performed in order to enable accurate, objective and highly automated protein structure determination by NMR.

copick

is a cross-platform, storage-agnostic and server-less dataset API for cryoET datasets. Access to the data is provided through an object-oriented API that abstracts away the underlying storage using the fsspec-family of libraries.

pdb-tools

a swiss army knife for manipulating and editing PDB files.

haddock-restraints

generates restraint files and related restraint information for HADDOCK docking workflows. It provides command-line tools for creating TBL files, true-interface restraints from PDB files, unambiguous restraints to keep molecules together during docking, interface residue lists, and Z-restraints for protein docking.

SBGrid Installer

Volume_Seg_Tool

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

HAX

is a package that includes several tools to study conformational heterogeneity from CryoEM data.

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.

OpenFreeEnergy

is a Python package for executing alchemical free energy calculations.

TEMPy-ReFF

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

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.