Sali Lab

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81 repositories

imp
Public
The Integrative Modeling Platform
structural-biology protein-structure integrative-modeling python c-plus-plus
C++
•
GNU General Public License v3.0
•30•76•64•1•Updated Feb 11, 2025Feb 11, 2025
saliweb
Public
Simple framework for web services in the Sali lab
perl-cgi web-framework python
Python
•
GNU Lesser General Public License v2.1
•3•5•1•0•Updated Feb 11, 2025Feb 11, 2025
IHMValidation
Public
Validation software for integrative models deposited to PDB
HTML
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MIT License
•2•2•32•1•Updated Feb 10, 2025Feb 10, 2025
imp_nightly_builds
Public
Infrastructure to build and test IMP on a nightly basis
Python
•
Creative Commons Attribution Share Alike 4.0 International
•0•0•0•0•Updated Feb 4, 2025Feb 4, 2025
imp_spatiotemporal_tutorial
Public
Tutorial for computing spatiotemporal integrative models in IMP
Python
•
Creative Commons Attribution Share Alike 4.0 International
•0•0•0•0•Updated Feb 3, 2025Feb 3, 2025
pmi
Public
Python Modeling Interface
structural-biology protein-structure integrative-modeling python
Python
•11•13•37•1•Updated Feb 1, 2025Feb 1, 2025
rmf
Public
The library to support reading and writing of RMF files.
python structural-biology protein-structure integrative-modeling c-plus-plus
C++
•
Apache License 2.0
•0•9•7•0•Updated Jan 31, 2025Jan 31, 2025
cryptosite
Public
Library for prediction of cryptic binding sites
protein-structure binding-sites prediction
Python
•
GNU Lesser General Public License v2.1
•5•20•0•0•Updated Jan 22, 2025Jan 22, 2025
SimPathFinder
Public
Predicting enzymatic pathways from partially/fully annotates enzymes.
Python
•
MIT License
•0•0•0•0•Updated Jan 21, 2025Jan 21, 2025
npctransport
Public
IMP module for simulating transport through the NPC.
C++
•2•3•6•0•Updated Jan 21, 2025Jan 21, 2025
SSEThread
Public
Integrative threading of protein structure using secondary structure elements
Python
•
GNU Lesser General Public License v2.1
•0•0•0•0•Updated Jan 21, 2025Jan 21, 2025
systems-web
Public
Web application to show integrative modeling "systems" pages
Python
•
MIT License
•0•0•0•0•Updated Jan 21, 2025Jan 21, 2025
imp-sampcon
Public
Scripts to assess sampling convergence and exhaustiveness
Python
•
GNU General Public License v2.0
•7•3•4•1•Updated Jan 21, 2025Jan 21, 2025
bayesian_hdx
Public
Support code for HDX data reduction
Python
•
GNU Lesser General Public License v2.1
•3•3•5•1•Updated Jan 21, 2025Jan 21, 2025
optrep
Public
IMP module for optimal coarse-grained bead representation
Python
•
GNU Lesser General Public License v2.1
•1•0•5•0•Updated Jan 21, 2025Jan 21, 2025
developer_tools
Public
🛠 Useful scripts used by several projects.
cmake build-tools python
Python
•
GNU Lesser General Public License v2.1
•0•0•2•0•Updated Jan 21, 2025Jan 21, 2025
threading
Public
IMP module to sample sequence threading
Python
•0•1•0•1•Updated Jan 21, 2025Jan 21, 2025
mist
Public
Mass spectrometry interaction STatistics
mass-spectrometry
Python
•
GNU Lesser General Public License v3.0
•0•1•1•0•Updated Jan 21, 2025Jan 21, 2025
pyRMSD
Public
pyRMSD is a small Python package that aims to offer an integrative and efficient way of performing RMSD calculations of large sets of structures. It is specially tuned to do fast collective RMSD calculations, as pairwise RMSD matrices.
C++
•
Other
•14•4•0•0•Updated Jan 21, 2025Jan 21, 2025
tutorial_tools
Public
🛠 Support infrastructure useful for all IMP tutorials
python tutorial build-tools
Python
•
GNU Lesser General Public License v2.1
•0•0•0•0•Updated Jan 21, 2025Jan 21, 2025
domino3
Public
Experimental DOMINO variant using traditional inference
C++
•
GNU Lesser General Public License v2.1
•0•1•0•0•Updated Jan 21, 2025Jan 21, 2025
imp_valgrind_tutorial
Public
Tutorial on debugging IMP code with Valgrind
c-plus-plus tutorial integrative-modeling
CMake
•
Creative Commons Attribution Share Alike 4.0 International
•0•0•0•0•Updated Jan 21, 2025Jan 21, 2025
imp_using_cpp_tutorial
Public
Tutorial on using IMP as a library in other C++ projects
c-plus-plus tutorial integrative-modeling
CMake
•
Creative Commons Attribution Share Alike 4.0 International
•0•0•0•0•Updated Jan 21, 2025Jan 21, 2025
imp_coding_tutorial
Public
Introduction to writing IMP code
c-plus-plus tutorial integrative-modeling
Python
•
Creative Commons Attribution Share Alike 4.0 International
•0•0•0•0•Updated Jan 21, 2025Jan 21, 2025
foxs_tutorial
Public
Tutorial for fitting against SAXS data using FoXS and MultiFoXS
tutorial command-line small-angle-xray integrative-modeling
Jupyter Notebook
•
Creative Commons Attribution Share Alike 4.0 International
•0•0•0•0•Updated Jan 21, 2025Jan 21, 2025
imp_brownian_dynamics_tutorial
Public
Tutorial for running Brownian dynamics simulations using IMP
tutorial integrative-modeling brownian-dynamics
Jupyter Notebook
•
Creative Commons Attribution Share Alike 4.0 International
•1•0•0•0•Updated Jan 21, 2025Jan 21, 2025
imp_analysis_tutorial
Public
Python
•
Other
•2•0•1•0•Updated Jan 21, 2025Jan 21, 2025
cross_linking_tutorial
Public
Introduction to working with cross-linking data using IMP
tutorial structural-biology integrative-modeling binder-ready
Jupyter Notebook
•
Creative Commons Attribution Share Alike 4.0 International
•0•1•0•0•Updated Jan 21, 2025Jan 21, 2025
actin_tutorial
Public
IMP/PMI tutorial, modeling the complex of actin and tropomodulin-gelsolin chimera
tutorial integrative-modeling
Python
•
Creative Commons Attribution Share Alike 4.0 International
•0•0•1•0•Updated Jan 21, 2025Jan 21, 2025
imp_tutorial
Public
Tutorial that demonstrates the modeling of RNA Polymerase II using Electron Microscopy density and chemical crosslinks
integrative-modeling python tutorial
Python
•
Creative Commons Attribution Share Alike 4.0 International
•5•3•1•1•Updated Jan 21, 2025Jan 21, 2025