Repositories list

• ChimeraX

  Public
  Source code for molecular graphics program UCSF ChimeraX

  Python

  •

  Other

  •41•224•5•55•Updated Feb 11, 2026Feb 11, 2026

• openfold-3

  Public
  A fully open source biomolecular structure prediction model based on AlphaFold3

  Python

  •

  Apache License 2.0

  •69•0•0•0•Updated Feb 10, 2026Feb 10, 2026

• qtshim

  Public
  ChimeraX's Qt shim library

  Python

  •0•0•0•0•Updated Feb 7, 2026Feb 7, 2026

• boltz

  Public
  Boltz-1 installed by ChimeraX Boltz tool

  Python

  •

  MIT License

  •744•0•0•0•Updated Jan 8, 2026Jan 8, 2026

• duo_unix

  Public
  Duo two-factor authentication for Unix systems

  C

  •148•0•0•0•Updated Dec 29, 2025Dec 29, 2025

• medical_imaging

  Public
  A ChimeraX bundle for medical imaging, intended for research purposes only

  Python

  •0•0•0•0•Updated Dec 20, 2025Dec 20, 2025

• chimerax-recipes

  Public
  Python

  •3•17•0•0•Updated Nov 19, 2025Nov 19, 2025

• LookSee

  Public
  LookSee molecular viewer for Quest VR headsets

  C#

  •1•2•11•0•Updated Oct 31, 2025Oct 31, 2025

• ColabFold

  Public
  Improvements to colabfold_search MSA calculation.

  Jupyter Notebook

  •

  MIT License

  •694•0•0•0•Updated Sep 21, 2025Sep 21, 2025

• stringApp

  Public
  Cytoscape interface to STRING and STITCH

  Java

  •

  BSD 2-Clause "Simplified" License

  •11•11•10•0•Updated May 9, 2025May 9, 2025

• readcif

  Public
  A fast C++ CIF and mmCIF parser

  C++

  •

  Other

  •3•8•1•0•Updated Apr 22, 2025Apr 22, 2025

• appstore

  Public
  Cytoscape App Store web application code

  Python

  •20•0•0•0•Updated Apr 10, 2025Apr 10, 2025

• ChimeraX-ScholAR

  Public
  Interface between ChimeraX and Schol-AR. Allows for creating and editing Schol-Ar projects and augmentations inside of ChimeraX.

  Python

  •1•0•0•0•Updated Nov 14, 2024Nov 14, 2024

• chemViz2

  Public
  Cheminformatics App for Cytoscape 3

  Java

  •4•7•6•2•Updated Nov 2, 2024Nov 2, 2024

• CyAnimator

  Public
  Key frame animation app for Cytoscape

  Java

  •3•4•3•0•Updated Oct 24, 2024Oct 24, 2024

• localizer

  Public
  Java

  •1•0•0•0•Updated Oct 24, 2024Oct 24, 2024

• ChimeraX-Bundle-Template-TOML

  Public template
  Makefile

  •1•1•0•0•Updated Sep 28, 2024Sep 28, 2024

• dovecot-submission

  Public
  Limit access to mail submission port to dovecot users using firewalld

  Python

  •0•0•0•0•Updated Aug 30, 2024Aug 30, 2024

• SPOKEApp

  Public
  Cytoscape interface to SPOKE

  Java

  •0•0•0•0•Updated Jul 19, 2024Jul 19, 2024

• CyPlot

  Public
  Java

  •3•3•2•0•Updated Jun 5, 2024Jun 5, 2024

• scNetViz

  Public
  Single-Cell RNA Seq analysis and visualization package for Cytoscape

  Java

  •

  Apache License 2.0

  •6•6•12•2•Updated May 3, 2024May 3, 2024

• ppeclient

  Public
  Python client for Proofpoint Essentials

  Makefile

  •0•0•0•0•Updated Aug 15, 2023Aug 15, 2023

• clusterMaker2

  Public
  Cytoscape 3 Clustering App

  Java

  •14•9•8•3•Updated Jun 16, 2023Jun 16, 2023

• rainloop-webmail

  Public
  Simple, modern & fast web-based email client

  PHP

  •

  MIT License

  •973•0•0•0•Updated Mar 9, 2023Mar 9, 2023

• mapSourceAndTarget

  Public
  Java

  •1•0•0•0•Updated Jan 6, 2023Jan 6, 2023

• ChimeraX-Bundle-Template

  Public template
  A template repository for prospective bundle developers

  Makefile

  •1•0•0•0•Updated Oct 6, 2022Oct 6, 2022

• minrms

  Public
  A bioinformatics algorithm for generating sequence alignments from 3D structures

  bioinformaticsprotein-structuresequence-alignment+ 2structure-alignmentstructural-bioinformatics

  C++

  •

  Other

  •2•4•1•0•Updated Feb 22, 2022Feb 22, 2022

• clusterJob

  Public
  A sample implementation of the Cytoscape jobs-api that mocks up a remote cluster service.

  Java

  •1•1•0•1•Updated Jun 4, 2021Jun 4, 2021

• structureVizX

  Public
  structureViz for ChimeraX

  Java

  •1•2•0•1•Updated Jun 4, 2021Jun 4, 2021

• enhancedGraphics

  Public
  App to add enhanced node graphics to Cytoscape 3

  Java

  •5•7•2•0•Updated Mar 31, 2021Mar 31, 2021