Skip to content

@Gallicchio-Lab Gallicchio-Lab

Change the repository type filter

All

    Repositories list

    23 repositories

    • openmm

      Public
      OpenMM is a toolkit for molecular simulation using high performance GPU code.
      C++
      •534•0•0•0•Updated Jan 22, 2025Jan 22, 2025

    • coordinate-swapping-method

      Public
      Simulation input files for the paper: Relative Binding Free Energy Estimation of Congeneric Ligands and Macromolecular Mutants with the Alchemical Transfer with Coordinate Swapping Method
      R
      •
      Creative Commons Zero v1.0 Universal
      •0•0•0•0•Updated Jan 20, 2025Jan 20, 2025

    • AToM-OpenMM

      Public
      OpenMM-based framework for absolute and relative binding free energy calculations with the Alchemical Transfer Method
      Python
      •
      Other
      •30•126•3•1•Updated Jan 20, 2025Jan 20, 2025

    • alchemical-best-practices

      Public
      Best practice document for alchemical free energy calculations going to livecoms journal
      Jupyter Notebook
      •
      Creative Commons Attribution 4.0 International
      •18•1•0•0•Updated Dec 26, 2024Dec 26, 2024

    • analytical-model-transfer

      Public
      Analytical model of coupling with corresponding data and optimized parameters to construct analytical model of transfer.
      Mathematica
      •0•0•0•0•Updated Oct 10, 2024Oct 10, 2024

    • receptor-hopping

      Public
      Simulation input files for the paper "Binding Selectivity Analysis from Alchemical Receptor Hopping and Swapping Free Energy Calculations"
      R
      •0•3•0•0•Updated Aug 23, 2024Aug 23, 2024

    • self-rbfe

      Public
      Simulation Input files for self-RBFE project
      R
      •1•0•0•0•Updated May 11, 2024May 11, 2024

    • femodel-tf-optimizer

      Public
      Maximum likelihood estimation with TensorFlow of the parameters of an analytical model of alchemical molecular binding
      maximum-likelihood-estimationalchemical-free-energy-calculationsmolrcular-bindingtensorflow
      Python
      •2•0•0•0•Updated May 2, 2024May 2, 2024

    • openmm-hip

      Public
      C
      •7•0•0•0•Updated Apr 15, 2024Apr 15, 2024

    • diffnet-tf

      Public
      Extended DiffNet implementation with TensorFlow 2
      Python
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Dec 30, 2023Dec 30, 2023

    • femto

      Public
      A comprehensive toolkit for predicting free energies
      Python
      •
      MIT License
      •8•0•0•0•Updated Dec 7, 2023Dec 7, 2023

    • ATM_MerckSet

      Public
      The structural and input files for ATM RBFE on Mecrk Dataset
      Python
      •
      MIT License
      •2•0•0•0•Updated Nov 30, 2023Nov 30, 2023

    • openmm-atmmetaforce-plugin

      Public
      An OpenMM plugin that implements the Alchemical Transfer Potential
      C++
      •
      GNU Lesser General Public License v2.1
      •7•37•1•0•Updated Apr 27, 2023Apr 27, 2023

    • openmm-atmmetaforce-plugin-feedstock

      Public
      A conda-smithy repository for openmm-atmmetaforce-plugin.
      Batchfile
      •
      BSD 3-Clause "New" or "Revised" License
      •3•0•0•0•Updated Apr 1, 2023Apr 1, 2023

    • SAMPL9-bCD

      Public
      A place where to share SAMPL9 bCD challenge input files etc.
      Python
      •1•0•0•0•Updated Feb 27, 2023Feb 27, 2023

    • 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
      •5.1k•0•0•0•Updated Jun 15, 2022Jun 15, 2022

    • SAMPL9

      Public
      Jupyter Notebook
      •
      Other
      •5•0•0•0•Updated Dec 9, 2021Dec 9, 2021

    • ATM-relative-binding-free-energy-paper

      Public
      0•1•0•0•Updated Nov 18, 2021Nov 18, 2021

    • alchemical-transfer-method

      Public
      Simulation input files for the paper Alchemical Transfer Approach to Absolute Binding Free Energy Estimation.
      Shell
      •3•2•0•0•Updated Oct 22, 2021Oct 22, 2021

    • openmm_sdm_plugin

      Public
      OpenMM plugin to implement single-decoupling method in alchemical free energy calculations
      C++
      •
      Other
      •3•1•0•0•Updated Sep 27, 2021Sep 27, 2021

    • openmm_sdm_workflow

      Public
      Example of the use of the single-decoupling method setup workflow
      openmmalchemical-free-energy-calculationssingle-decouplingmolecular-binding
      Python
      •4•2•0•0•Updated Apr 13, 2021Apr 13, 2021

    • water-droplet-hydration

      Public
      A repository of simulation files for water-droplet and solute complexes.
      Shell
      •0•2•0•0•Updated Jan 16, 2021Jan 16, 2021

    • openmm_agbnp_plugin

      Public
      An OpenMM plugin implementing the AGBNP implicit solvent model
      agbnp-modelgaussvol-modelopenmmopenmm-plugin
      C++
      •
      Other
      •1•6•0•0•Updated Oct 26, 2019Oct 26, 2019