Jul 22 2025
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DIALS
(Diffraction Integration for Advanced Light Sources) a software project for the analysis of crystallographic diffraction images for many new methods from shutterless, fine-sliced rotation scans to randomly-oriented snapshots of serial crystallography. It uses multiple CPU and GPU machines to increase speed and accuracy based on a comprehensive physical model.
Updated versions:
3.25.0 | Linux 64
3.21.1 | Linux 64
3.19.0 | Linux 64
3.18.0 | Linux 64
3.17.0 | Linux 64
3.14.2 | Linux 64
3.13.0 | Linux 64
2.2.3 | Linux 64
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Jul 18 2025
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UGENE
UGENE is a free open-source bioinformatics software
for macOS, and Linux.
Updated versions:
52.1 | Linux 64
52.1 | OS X INTEL
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Jul 18 2025
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RDKit
a collection of cheminformatics and machine-learning software written in C++ and Python.
Updated versions:
2025.03.4 | Linux 64
2025.03.4 | OS X INTEL
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Jul 17 2025
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DenoisET
is an implementation of the Noise2Noise algorithm specifically designed for cryoET data denoising. The software streamlines integration with AreTomo3 and provides automated tomogram selection for training and inference transition decisions to avoid overdenoising artifacts. It can operate during live data collection, either applying pre-trained models or training new 3D denoising models from scratch using CTF-deconvolved tomograms.
Updated versions:
0.1.0 | Linux 64
0.1.0 | OS X INTEL
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Jul 17 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:
2.2.2 | Linux 64
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Jul 17 2025
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ORCA
an electronic structure program package that is a flexible, efficient, and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules.
Updated versions:
6.1.0_intel | OS X INTEL
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Jul 17 2025
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POKY
a software suite for multidimensional NMR and 3D structure calculation of biomolecules.
Updated versions:
20250618 | Linux 64
20250618 | OS X INTEL
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Jul 17 2025
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Julia
a flexible dynamic language appropriate for scientific and numerical computing with performance comparable to traditional statically-typed languages.
Updated versions:
1.11.6 | Linux 64
1.11.6_arm | OS X INTEL
1.11.6_intel | OS X INTEL
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Jul 16 2025
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BioEmu
is a model that samples from the approximated equilibrium distribution of structures for a protein monomer, given its amino acid sequence.
Updated versions:
0.1.12 | Linux 64
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Jul 15 2025
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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.
Updated versions:
1.22 | Linux 64
1.22 | OS X INTEL
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Jul 15 2025
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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.
Updated versions:
1.22.1 | Linux 64
1.22.1 | OS X INTEL
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Jul 15 2025
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ORCA
an electronic structure program package that is a flexible, efficient, and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules.
Updated versions:
6.1.0 | Linux 64
6.1.0_arm | OS X INTEL
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Jul 15 2025
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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.
Updated versions:
3.7.1 | Linux 64
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Jul 15 2025
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Xmipp
(X-Window-based Microscopy Image Processing Package) a suite of image processing programs primarily aimed at single-particle 3D electron microscopy.
Updated versions:
3.24.12.2 | Linux 64
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Jul 14 2025
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SBGrid Installer
an application for managing an SBGrid software installation. Users can choose a subset of applications for installation on their laptops or desktops or configure site installations for clusters, servers or cloud resources. This version is the command-line interface. A graphical version is available for download on the SBGrid wiki : https://sbgrid.org/wiki/client_downloads .
Updated versions:
2.12.3 | Linux 64
2.12.3 | OS X INTEL
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Jul 14 2025
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Xmipp
(X-Window-based Microscopy Image Processing Package) a suite of image processing programs primarily aimed at single-particle 3D electron microscopy.
Updated versions:
3.25.06 | Linux 64
|
Jul 10 2025
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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.
Updated versions:
0.3.11 | Linux 64
|
Jul 10 2025
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IntelliFold
a controllable foundation model for general and specialized biomolecular structure prediction that supports proteins, nucleic acids, and their complexes.
Updated versions:
0.1.4 | Linux 64
|
Jul 09 2025
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Schrodinger
a suite of tools for drug discovery.
Updated versions:
2025-2 | Linux 64
2025-2 | OS X INTEL
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Jul 09 2025
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FoldBench
a comprehensive all-atom benchmark for biomolecular structure prediction that spans proteins, nucleic acids, ligands, and six major interaction types.
Updated versions:
20250709 | Linux 64
|
Jul 09 2025
|
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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Jul 09 2025
|
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.
Updated versions:
2.2.9 | Linux 64
2.2.9 | OS X INTEL
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Jul 09 2025
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OpenMM
a high performance toolkit for molecular simulation that can be used either as a stand-alone application for running simulations or as a library you call from your own code.
Updated versions:
8.3.0 | Linux 64
8.3.0 | OS X INTEL
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Jul 08 2025
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IPA
a program for ab initio phase determination.
Updated versions:
1.2.1 | OS X INTEL
|
Jul 07 2025
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aitom
an open-source platform for AI driven cellular electron cryo-tomography analysis.
AITom is originated from the tomominer library, adapted from an extended version of the tomominer library, developed at Alber Lab.
Updated versions:
0.0.1 | Linux 64
|
Jul 06 2025
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Schrodinger
a suite of tools for drug discovery.
Updated versions:
2024-3 | OS X INTEL
2024-4 | OS X INTEL
2024-2 | OS X INTEL
2025-1 | OS X INTEL
2025-1 | Linux 64
2024-2 | Linux 64
2024-4 | Linux 64
2024-3 | Linux 64
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Jul 03 2025
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PHENIX
(Python-based Hierarchical Environment for INtegrated Xtallography) a software suite for the automated determination of molecular structures using X-ray crystallography and other methods.
Updated versions:
1.21.2-5419 | OS X INTEL
1.21.2-5419 | Linux 64
|
Jul 03 2025
|
DIALS
(Diffraction Integration for Advanced Light Sources) a software project for the analysis of crystallographic diffraction images for many new methods from shutterless, fine-sliced rotation scans to randomly-oriented snapshots of serial crystallography. It uses multiple CPU and GPU machines to increase speed and accuracy based on a comprehensive physical model.
Updated versions:
3.25.0 | OS X INTEL
|
Jul 03 2025
|
cryoPROS
a computational framework specifically designed to tackle misalignment errors caused by preferred orientation issues in single-particle cryo-EM.
Updated versions:
1.0.1 | Linux 64
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Jul 01 2025
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PowerFit
a Python package and simple command-line program to automatically fit high-resolution atomic structures in cryo-EM densities.
Updated versions:
3.0.2 | Linux 64
3.0.2 | OS X INTEL
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