Software Updates

GetContacts

is designed to dissect and visualize molecular interactions in proteins from various sources, including experimental structures (X-ray, NMR, Cryo-EM) and MD simulations. It helps identify key residues and interaction networks, and how these change across different states, conditions, or protein families. It can compare static structures, analyze ensembles from simulations, identify simulation substates, and facilitate large-scale interaction analysis.

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.

MODELLER

a tool used for homology or comparative modeling of protein three-dimensional structures. From a sequence alignment with known related structures, MODELLER automatically calculates a model containing all non-hydrogen atoms using comparative protein structure modeling by satisfaction of spatial restraints. It can also perform de novo modeling of loops in protein structures and optimize various models of protein structure with respect to a flexibly defined objective function, multiple alignment of protein sequences and/or structures, clustering, searching of sequence databases, comparison of protein structures, etc.

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.

DiffModeler

a diffusion model based protein complex structure modeling tool.

outlierremoval

Implementation of outlier removal in cryo-electron microscopy (cryo-EM) datasets using radial profiles. The method focuses on removing outliers to enhance the quality of the 2D class averages and downstream analysis.

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.

cryoPROS

a computational framework specifically designed to tackle misalignment errors caused by preferred orientation issues in single-particle cryo-EM.

AreTomo3

a multi-GPU accelerated software package that enables real-time fully automated reconstruction of cryoET tomograms in parallel with cryoET data collection.

PyEM

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

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.

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.

PSI4

is an open-source suite of ab initio quantum chemistry programs designed for efficient, high-accuracy simulations of molecular properties.

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.

LocScale

is an automated tool for physics-informed cryo-EM map optimisation (sharpening/density modification), improving interpretability using electron scattering properties derived from the map or an atomic model.

SPIDER

(System for Processing Image Data from Electron microscopy and Related fields) a large image processing suite for electron microscopy.

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.

XDS

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

ModelAngelo

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

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.

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.

BioEmu

is a model that samples from the approximated equilibrium distribution of structures for a protein monomer, given its amino acid sequence.

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.

MemBrain-Seg

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

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.

MemBrain-Seg

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

EMInfo

a deep learning framework for detecting the secondary structures of proteins and the region of nucleic acids in a cryo-EM map

AlphaFold

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

Follow_Relion_Gracefully

a complete dashboard for easy interaction with your cryo-EM data in Relion, now with full #teamtomo support!

R

a free software environment for statistical computing and graphics.

Xmipp

(X-Window-based Microscopy Image Processing Package) a suite of image processing programs primarily aimed at single-particle 3D electron microscopy.