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    40 repositories

    • alchemiscale-fah

      Public
      protocols and compute service for using alchemiscale with Folding@Home
      Python
      •
      MIT License
      •0•2•9•0•Updated Feb 15, 2025Feb 15, 2025

    • alchemiscale

      Public
      a high-throughput alchemical free energy execution system for use with HPC, cloud, bare metal, and Folding@Home
      Python
      •
      Other
      •8•25•68•10•Updated Feb 15, 2025Feb 15, 2025

    • openfe

      Public
      The Open Free Energy toolkit
      molecular-dynamicscomputational-chemistryfree-energybiophysicsfree-energy-calculations
      Python
      •
      MIT License
      •24•153•213•23•Updated Feb 14, 2025Feb 14, 2025

    • pontibus

      Public
      Experimental OpenFE Protocols for Force Field Evaluation
      Python
      •
      MIT License
      •0•0•32•0•Updated Feb 14, 2025Feb 14, 2025

    • gufe

      Public
      grand unified free energy by OpenFE
      Python
      •
      MIT License
      •10•35•89•17•Updated Feb 14, 2025Feb 14, 2025

    • ExampleNotebooks

      Public
      Notebooks demonstrating how to do simple tasks related to free energy calculations.
      Jupyter Notebook
      •
      MIT License
      •5•40•37•5•Updated Feb 14, 2025Feb 14, 2025

    • feflow

      Public
      Recipes and protocols for molecular free energy calculations using the openmmtools/perses and Open Free Energy toolkits
      Python
      •
      MIT License
      •1•11•45•5•Updated Feb 13, 2025Feb 13, 2025

    • IndustryBenchmarks2024

      Public
      Repository for the 2024 OpenFE industry benchmark efforts
      Python
      •
      MIT License
      •19•13•13•2•Updated Feb 12, 2025Feb 12, 2025

    • openfe-benchmarks

      Public
      Jupyter Notebook
      •
      MIT License
      •1•8•33•1•Updated Feb 11, 2025Feb 11, 2025

    • Lomap

      Public
      Alchemical mutation scoring map
      Python
      •
      MIT License
      •11•33•12•0•Updated Feb 11, 2025Feb 11, 2025

    • alchemiscale.org-site

      Public
      source files and deployment automation for the alchemiscale.org static site
      CSS
      •0•0•0•0•Updated Feb 11, 2025Feb 11, 2025

    • openfreeenergy.github.io

      Public
      HTML
      •2•1•13•2•Updated Feb 10, 2025Feb 10, 2025

    • openfe_analysis

      Public
      Python
      •
      MIT License
      •1•8•26•2•Updated Feb 3, 2025Feb 3, 2025

    • stratocaster

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Jan 31, 2025Jan 31, 2025

    • exorcist

      Public
      Daemonless campaign-scale simulation orchestration
      Python
      •
      MIT License
      •0•0•9•4•Updated Jan 26, 2025Jan 26, 2025

    • konnektor

      Public
      Algorithms for various Network Layouts and Tooling for planning FE Calculations
      pythonfree-energy-calculationsnetwork-planningopenfe
      Jupyter Notebook
      •
      MIT License
      •4•15•20•3•Updated Jan 15, 2025Jan 15, 2025

    • .github

      Public
      Default OpenFE community files
      MIT License
      •0•0•0•1•Updated Jan 15, 2025Jan 15, 2025

    • openfe-gromacs

      Public
      Gromacs-based protocols for Open Free Energy
      Python
      •
      MIT License
      •0•1•21•2•Updated Jan 13, 2025Jan 13, 2025

    • kartograf

      Public
      This package contains tools for setting up hybrid-topology FE calculations
      pythonfree-energy-calculationshybrid-topologyopenfeatom-mapping
      Python
      •
      MIT License
      •4•26•13•2•Updated Jan 10, 2025Jan 10, 2025

    • cinnabar

      Public
      Package for consistent reporting of relative free energy results
      Python
      •
      MIT License
      •13•37•45•7•Updated Jan 7, 2025Jan 7, 2025

    • openmmtools

      Public
      A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.
      Python
      •
      MIT License
      •83•2•0•0•Updated Jan 7, 2025Jan 7, 2025

    • alchemiscale.org-deployment

      Public
      deployment versioning and artifact generation for alchemiscale.org alchemiscale instances
      Dockerfile
      •
      MIT License
      •0•0•4•0•Updated Dec 31, 2024Dec 31, 2024

    • ofe-sphinx-theme

      Public
      Sphinx theme for Open Free Energy software based on the PyData theme.
      SCSS
      •
      MIT License
      •0•1•1•0•Updated Oct 31, 2024Oct 31, 2024

    • protein-ligand-benchmark

      Public
      Protein-Ligand Benchmark Dataset for Free Energy Calculations
      Python
      •
      MIT License
      •16•1•3•0•Updated Jul 1, 2024Jul 1, 2024

    • OMSF_workshop2024

      Public
      Materials and assets for the 2024 OMSF workshop
      MIT License
      •0•5•0•0•Updated May 16, 2024May 16, 2024

    • openfe_skunkworks

      Public
      experimental toybox
      Python
      •
      MIT License
      •1•3•2•1•Updated Apr 18, 2024Apr 18, 2024

    • pdbinf

      Public
      Python
      •
      MIT License
      •0•7•2•0•Updated Mar 23, 2024Mar 23, 2024

    • validation-benchmarks

      Public
      Validation benchmark sets for free energy calculations
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Nov 2, 2023Nov 2, 2023

    • SeparatedTopologies

      Public
      Exploratory work on free energy calculations with GROMACS using "separated topologies" approach (Rocklin et al., 2013).
      Python
      •
      MIT License
      •8•0•0•0•Updated Sep 14, 2023Sep 14, 2023

    • openff-toolkit

      Public
      The Open Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools. Documentation available at http://open-forcefield-toolkit.readthedocs.io
      Jupyter Notebook
      •
      MIT License
      •94•1•0•0•Updated Jul 17, 2023Jul 17, 2023