Software Updates

CryoFold

a graphical user interface for the CryoFold method, which integrates several computational techniques (MAINMAST, Targeted Molecular Dynamics, MDFF/ReMDFF, and MELD) to determine protein structures and conformational ensembles from cryo-EM density maps.

Chai-1

a multi-modal foundation model for molecular structure prediction that performs at the state-of-the-art across a variety of benchmarks. Chai-1 enables unified prediction of proteins, small molecules, DNA, RNA, glycosylations, and more.

CryoVia

an image analysis toolkit for the quantification of membrane structures from cryo-EM micrographs

RosettaDDGPrediction

is a Python package to run Rosetta-based protocols for the prediction of the ΔΔG of stability upon mutation of a monomeric protein or the ΔΔG of binding upon mutation of a protein complex and analyze the results.

cryo-MEM

a software for membrane signal subtraction to facilitate high-resolution cryo-EM reconstruction of membrane proteins embedded in their native membrane environment.

miffi

a tool for Cryo-EM micrograph filtering utilizing Fourier space information

tomoCPT

is a deep learning based program for enabling centroid prediction of objects in 3D cryo-tomograms.

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.

pdb_extract

a program suite that contains tools and examples for extracting data from many structure determination applications and assembles the data into mmCIF format for wwPDB deposition.

NuFold

a state-of-the-art method designed for predicting 3D RNA structures, leveraging deep learning for high accuracy and reliability. This tool is particularly useful for biologists and bioinformatics researchers focusing on RNA function and structure.

JupyterLab

a program for the next-generation web-based user interface for Project Jupyter. JupyterLab enables you to work with documents and activities such as Jupyter notebooks, text editors, terminals, and custom components in a flexible, integrated, and extensible manner.

AlphaPulldown

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

SIREn

a toolkit for analyzing heterogeneity in 3D volume ensembles generated via cryo-EM. SIREn performs automated detection of structural blocks to allow model-free detection of heterogeneity, and additionally includes a 3D Convolutional Neural Network (CNN) to predict binarization thresholds for 3D density maps.

RECOVAR

a software tool for analyzing different conformations in heterogeneous cryo-EM and cryo-ET datasets. RECOVAR can reconstruct high-resolution volumes, estimate conformational density and low free-energy motions, and automatically identify subsets of images with a particular volume feature.

Warp

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

IDPConformerGenerator

(Intrinsically Disordered Proteins Conformer Generator) a flexible, modular platform for generating ensembles of disordered protein states that builds conformers by sampling backbone torsion angles of relevant sequence fragments extracted from protein structures in the RCSB Protein Data Bank.

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.

HPN-SSH

a high performance soft fork of OpenSSH that can provide significnatly faster throughput for bulk data transfers over a wide range of network paths.

MDCatch

is a simple app to fetch acquisition metadata from a EPU session or SerialEM. It parses the first found xml/mdoc/mrc/tif file (from EPU/SerialEM) associated with a data collection session and launches Relion 4 or Scipion 3 pipeline.

cs2star

a simple utility that wraps around csparc2star.py to convert particle positions from Cryosparc JOB directories into a RELION-ready directory.

RDKit

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

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.

PROPKA

a tool that predicts the pKa values of ionizable groups in proteins (version 3.0) and protein-ligand complexes (version 3.1 and later) based on the 3D structure.

MAVEn

is a tool for the systematic analysis of compositionally-heterogeneous cryo-EM datasets. MAVEn is designed to work downstream of cryoDRGN, after users have generated a large number of maps (usually 500-1000) systematically sampling the latent space, but can be applied to any ensemble of volumes.

VISDEM

is a cryo‑EM density map sharpening tool that estimates the underlying atomic distribution of a protein from the density map and computes the corresponding radially averaged structure factor and density histogram.

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.

RELION composite masks

a RELION 4 and 5 with support for composite masks