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Sali Lab · GitHub

Laboratory of Andrej Sali at the University of California San Francisco

We aim to develop and apply computational methods for integrative determination of the structures and dynamics of macromolecular assemblies, in turn informing the function and evolution of these systems as well as how to modulate them. The broad goal is to contribute to a predictive spatiotemporal model of the cell. This goal is being achieved by a formal integration of experiment, physics, and statistical inference, spanning all relevant size and time scales. Our computational methods are implemented in the open source Integrative Modeling Platform package (IMP) and the resulting models are deposited in the PDB-Dev database. This research enhances the discovery of general principles that underlie all cellular processes, which in turn also facilitates drug discovery.

1. The Integrative Modeling Platform

   C++ 77 31

2. Python Modeling Interface

   Python 13 12

3. The library to support reading and writing of RMF files.

   C++ 9

• salilab/homebrew-salilab’s past year of commit activity Ruby 1 CC-BY-SA-4.0 0 0 0 Updated Aug 17, 2025
• IHMValidation Public

  Validation software for integrative models deposited to PDB

  salilab/IHMValidation’s past year of commit activity Python 3 MIT 2 15 1 Updated Aug 15, 2025
• imp Public

  The Integrative Modeling Platform

  salilab/imp’s past year of commit activity C++ 77 GPL-3.0 31 63 1 Updated Aug 13, 2025
• emseqfinder Public

  Assignment of primary sequence to backbone fragments traced in a cryo-EM map

  salilab/emseqfinder’s past year of commit activity Jupyter Notebook 0 1 0 0 Updated Aug 13, 2025
• salilab/allosmod-lib’s past year of commit activity Python 5 LGPL-2.1 0 0 0 Updated Aug 6, 2025
• cryptosite Public

  Library for prediction of cryptic binding sites

  salilab/cryptosite’s past year of commit activity Python 23 LGPL-2.1 5 0 0 Updated Aug 6, 2025
• salilab/imp_nightly_builds’s past year of commit activity Python 0 CC-BY-SA-4.0 0 0 0 Updated Aug 5, 2025
• npctransport Public

  IMP module for simulating transport through the NPC.

  salilab/npctransport’s past year of commit activity C++ 3 3 6 0 Updated Jul 23, 2025
• systems-web Public

  Web application to show integrative modeling "systems" pages

  salilab/systems-web’s past year of commit activity Python 0 MIT 0 0 0 Updated Jul 23, 2025
• multifoxs Public

  Web server for multi-state modeling with SAXS profiles

  salilab/multifoxs’s past year of commit activity Python 1 LGPL-2.1 2 0 0 Updated Jul 21, 2025

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