Apr 24 2025
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cryomem
A software for membrane signal subtraction to facilitate high-resolution cryo-EM reconstruction of membrane proteins embedded in their native membrane environment.
Updated versions:
3dff057 | Linux 64
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Apr 24 2025
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miffi
Cryo-EM micrograph filtering utilizing Fourier space information
Updated versions:
1.0.0 | Linux 64
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Apr 23 2025
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R
a free software environment for statistical computing and graphics.
Updated versions:
4.4.2 | OS X INTEL
4.4.2 | Linux 64
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Apr 22 2025
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tomocpt
tomoCPT (tomogram Centroid Prediction Tool) is a deep learning based program for enabling centroid prediction of objects in 3D cryo-tomograms.
Updated versions:
23f0a2b | Linux 64
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Apr 16 2025
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AreTomo3
a multi-GPU accelerated software package that enables real-time fully automated reconstruction of cryoET tomograms in parallel with cryoET data collection.
Updated versions:
2.1.3 | Linux 64
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Apr 16 2025
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NMRFx Structure
NMRFx Structure can be used to generate and analyze macromolecular structures and predict chemical shifts.
Updated versions:
11.1.37 | Linux 64
11.1.37 | OS X INTEL
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Apr 16 2025
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NMRFx Analyst
a tool for NMR processing, visualization and analysis that
Integrates code of NMRFx Processor, Structure and additional tools
Updated versions:
11.4.20 | Linux 64
11.4.20 | OS X INTEL
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Apr 16 2025
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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.
Updated versions:
4.3 | Linux 64
4.3 | OS X INTEL
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Apr 16 2025
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nufold
NuFold is 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.
Updated versions:
1.0 | Linux 64
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Apr 16 2025
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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.
Updated versions:
4.4.0 | Linux 64
4.4.0 | OS X INTEL
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Apr 11 2025
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AlphaPulldown
a Python package that streamlines protein-protein interaction screens and high-throughput modelling of higher-order oligomers using AlphaFold-Multimer.
Updated versions:
2.0.3 | Linux 64
2.0.1 | Linux 64
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Apr 10 2025
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SIREn
SIREn is 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.
Updated versions:
1.0.0 | Linux 64
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Apr 08 2025
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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.
Updated versions:
0.4.4 | Linux 64
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Apr 07 2025
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Warp
a set of tools for cryo-EM and cryo-ET data processing including, among other tools: Warp, M, WarpTools, MTools, MCore, and Noise2Map.
Updated versions:
2.0.0dev33 | Linux 64
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Apr 07 2025
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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.
Updated versions:
0.7.25 | Linux 64
0.7.25 | OS X INTEL
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Apr 03 2025
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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.
Updated versions:
4.2 | Linux 64
4.2.1 | Linux 64
4.2.1 | OS X INTEL
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Apr 03 2025
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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.
Updated versions:
0.6.1 | Linux 64
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Apr 03 2025
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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.
Updated versions:
18.6.2 | Linux 64
18.6.2 | OS X INTEL
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Apr 03 2025
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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.
Updated versions:
2.5 | Linux 64
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Apr 03 2025
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cs2star
a simple utility that wraps around csparc2star.py to convert particle positions from Cryosparc JOB directories into a RELION-ready directory.
Updated versions:
0.6.6 | Linux 64
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Apr 02 2025
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RDKit
a collection of cheminformatics and machine-learning software written in C++ and Python.
Updated versions:
2023.09 | Linux 64
2025.03.1 | Linux 64
2025.03.1 | OS X INTEL
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Apr 02 2025
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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.
Updated versions:
0.3.10 | Linux 64
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Apr 02 2025
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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.
Updated versions:
3.5.1 | Linux 64
3.5.1 | OS X INTEL
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Apr 01 2025
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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.
Updated versions:
1.0 | Linux 64
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Apr 01 2025
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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.
Updated versions:
1.2 | Linux 64
1.2 | OS X INTEL
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Apr 01 2025
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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.
Updated versions:
1.18.0 | Linux 64
1.18.0_arm | OS X INTEL
1.18.0 | OS X INTEL
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Apr 01 2025
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RELION composite masks
a RELION 4 tool with support for composite masks
Updated versions:
20250314_cu11.8 | Linux 64
20250314_cu12.2 | Linux 64
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