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    97 repositories

    • fes-ml

      Public
      Hybrid ML/MM free energy simulations.
      Python
      •
      GNU General Public License v3.0
      •0•5•1•0•Updated Mar 6, 2026Mar 6, 2026

    • CGRP_hydrocarbon_staples

      Public
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Mar 6, 2026Mar 6, 2026

    • PyXDM

      Public
      Python package for calculating XDM (Exchange-hole Dipole Moment) multipole moments using multiple atoms-in-molecules (AIM) partitioning schemes.
      dftquantum-chemistrydispersion
      dftquantum-chemistrydispersionxdmlennard-jonesc6exchange-holebecke-roussel
      Python
      •
      GNU General Public License v3.0
      •0•2•0•0•Updated Feb 24, 2026Feb 24, 2026

    • a3fe

      Public
      Automated Adaptive Absolute alchemical Free Energy calculator
      Python
      •
      GNU General Public License v3.0
      •14•114•16•3•Updated Feb 9, 2026Feb 9, 2026

    • EMLE_HFE_SI

      Public
      Figures and supporting data for "Enhancing Electrostatic Embedding for ML/MM Free Energy Calculations"
      Jupyter Notebook
      •0•0•0•0•Updated Dec 3, 2025Dec 3, 2025

    • RBFE-Benchmark

      Public
      Inputs, results, and pipeline code for Modular and Interoperable Workflows for Benchmarking Alchemical Binding Free Energy Calculation Methodologies manuscript.
      Jupyter Notebook
      •1•9•0•0•Updated Nov 24, 2025Nov 24, 2025

    • MDM2-PFEP

      Public
      Input files and instructions for reproducing results in the MDM2 alchemical side-chain mutation study
      Jupyter Notebook
      •1•0•1•0•Updated Nov 4, 2025Nov 4, 2025

    • Stapline

      Public
      A pipeline for the force field parameterisation and secondary structure analysis of stapled peptides
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •1•6•0•0•Updated Sep 24, 2025Sep 24, 2025

    • BioSimSpace

      Public
      Code and resources for the EPSRC BioSimSpace project.
      reproducible-researchmolecular-dynamicscomputational-biology
      reproducible-researchmolecular-dynamicscomputational-biologyinteroperabilitycomputational-chemistrycomputational-physicsreproducibilitybiomolecular-simulationccpbiosim
      Python
      •
      GNU General Public License v3.0
      •19•78•24•0•Updated Sep 1, 2025Sep 1, 2025

    • ABFE_MolecularGlues_Project

      Public
      Data and scripts for the summer project: "Absolute Binding Free Energy Calculations of Bivalent Molecular Glues"
      Jupyter Notebook
      •0•3•0•0•Updated Aug 1, 2025Aug 1, 2025

    • MDM2-D2O-paper

      Public
      Conformational ensembles from the MDM2 disorder-to-order mutants study
      MIT License
      •0•1•0•0•Updated Jun 29, 2025Jun 29, 2025

    • emle-bespoke

      Public
      A package for training and patching EMLE models, with routines for fitting LJ parameters.
      Python
      •
      GNU General Public License v3.0
      •0•5•0•0•Updated Jun 19, 2025Jun 19, 2025

    • CCmetaD

      Public
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Mar 28, 2025Mar 28, 2025

    • polaris-poses-challenge-fegrow-a3fe

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Mar 12, 2025Mar 12, 2025

    • AMMo

      Public
      Python
      •
      Apache License 2.0
      •1•8•0•0•Updated Mar 8, 2025Mar 8, 2025

    • fast_abfe

      Public
      Jupyter Notebook
      •
      MIT License
      •1•0•0•0•Updated Dec 26, 2024Dec 26, 2024

    • Robust-Equilibration-Detection-Paper

      Public
      Jupyter Notebook
      •
      MIT License
      •1•0•0•0•Updated Oct 10, 2024Oct 10, 2024

    • Automated-ABFE-Paper

      Public
      Inputs and code to reproduce the results and analysis from "Automated Adaptive Absolute Binding Free Energy Calculations"
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •3•4•0•0•Updated Oct 8, 2024Oct 8, 2024

    • idpabfe

      Public
      Scripts and datasets associated with alchemical ABFE and MSM ligand binding study to disordered c-Myc
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Jul 11, 2024Jul 11, 2024

    • EspalomaFFComparison

      Public
      Jupyter Notebook
      •0•0•1•0•Updated Jun 27, 2024Jun 27, 2024

    • RNA_AFE

      Public
      RNA AFE analysis for BSc Project
      Jupyter Notebook
      •0•0•0•0•Updated Mar 22, 2024Mar 22, 2024

    • BioSimSpaceTutorials

      Public
      10•25•0•0•Updated Jan 16, 2024Jan 16, 2024

    • ccgbsa

      Public
      Simulations of coiled coils with OpenMM
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•6•0•0•Updated Dec 18, 2023Dec 18, 2023

    • SireUnitTests

      Public
      Python
      •
      GNU General Public License v3.0
      •2•0•0•0•Updated Sep 11, 2023Sep 11, 2023

    • Sire

      Public
      Sire Molecular Simulations Framework
      C++
      •
      GNU General Public License v3.0
      •24•97•35•1•Updated Jul 17, 2023Jul 17, 2023

    • BioSimSpaceWebsite

      Public
      Files needed to configure the BioSimSpace website and associated Jupyter notebooks on Kubernetes
      Dockerfile
      •
      MIT License
      •0•1•0•0•Updated Feb 6, 2023Feb 6, 2023

    • openmmtools

      Public
      A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.
      Python
      •
      MIT License
      •85•0•0•0•Updated Jan 31, 2023Jan 31, 2023

    • Multiple-Distance-Restraints

      Public
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •2•5•0•0•Updated Jan 2, 2023Jan 2, 2023

    • BioSimSpaceCloud

      Public
      Files used to put BioSimSpace onto the cloud (via Fn functions)
      Python
      •
      Apache License 2.0
      •1•1•0•1•Updated Nov 16, 2022Nov 16, 2022

    • FreeEnergyNetworkAnalysis

      Public
      Software for automated processing of alchemical free energy calculations
      Python
      •6•11•5•0•Updated Nov 7, 2022Nov 7, 2022