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    88 repositories

    • a3fe

      Public
      Automated Adaptive Absolute alchemical Free Energy calculator
      Python
      •
      GNU General Public License v3.0
      •7•68•3•0•Updated Nov 28, 2024Nov 28, 2024

    • BioSimSpace

      Public
      Code and resources for the EPSRC BioSimSpace project.
      reproducible-researchmolecular-dynamicscomputational-biologyinteroperabilitycomputational-chemistrycomputational-physicsreproducibilitybiomolecular-simulationccpbiosim
      Python
      •
      GNU General Public License v3.0
      •19•77•24•0•Updated Nov 7, 2024Nov 7, 2024

    • RBFE-Benchmark

      Public
      Python
      •1•1•0•0•Updated Oct 28, 2024Oct 28, 2024

    • Robust-Equilibration-Detection-Paper

      Public
      Jupyter Notebook
      •
      MIT License
      •0•1•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•3•0•0•Updated Oct 8, 2024Oct 8, 2024

    • fast_abfe

      Public
      Jupyter Notebook
      •
      MIT License
      •1•0•0•0•Updated Oct 7, 2024Oct 7, 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

    • AMMo

      Public
      Python
      •
      Apache License 2.0
      •1•5•0•0•Updated May 23, 2024May 23, 2024

    • RNA_AFE

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

    • MDM2-D2O-paper

      Public
      Conformational ensembles from the MDM2 disorder-to-order mutants study
      MIT License
      •0•1•0•0•Updated Feb 24, 2024Feb 24, 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

    • Stapline

      Public
      A pipeline project for understanding and predict secondary structure of stapled peptides using REMD
      Python
      •1•3•0•0•Updated Oct 22, 2023Oct 22, 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
      •26•95•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
      •81•0•0•0•Updated Jan 31, 2023Jan 31, 2023

    • Multiple-Distance-Restraints

      Public
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•3•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•10•5•0•Updated Nov 7, 2022Nov 7, 2022

    • bssccpbiosim2022

      Public
      Material for the BioSimSpace workshop at the upcoming 2022 CCPBioSim Training Week
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •3•9•1•0•Updated Oct 11, 2022Oct 11, 2022

    • kcombu_bss

      Public
      Fork of the kcombu (BSD) program, aiming to make this easier to install on the range of platforms supported by BioSimSpace
      C
      •
      Other
      •2•0•0•0•Updated Sep 21, 2022Sep 21, 2022

    • RBFENN

      Public
      Jupyter Notebook
      •
      GNU General Public License v2.0
      •0•9•0•0•Updated Sep 19, 2022Sep 19, 2022

    • bgflow

      Public
      Boltzmann Generators and Normalizing Flows in PyTorch
      Jupyter Notebook
      •
      MIT License
      •36•1•0•0•Updated May 5, 2022May 5, 2022

    • MDM2-DG_paper

      Public
      Data and code to reproduce results in MDM2 disorder-order transition paper
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Dec 10, 2021Dec 10, 2021

    • bgflowexperiments

      Public
      Experiments with Boltzmann Generators
      GNU General Public License v3.0
      •0•0•0•0•Updated Oct 15, 2021Oct 15, 2021

    • Lomap_2021

      Public
      Python
      •
      MIT License
      •0•1•0•0•Updated Jul 9, 2021Jul 9, 2021

    • staged-recipes

      Public
      A place to submit conda recipes before they become fully fledged conda-forge feedstocks
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •5k•0•0•0•Updated Jul 2, 2021Jul 2, 2021

    • Custom_residus_parametrization

      Public
      Python
      •0•0•0•0•Updated Jun 8, 2021Jun 8, 2021