OpenMM-based framework for absolute and relative binding free energy calculations with the Alchemical Transfer Method
☆158Mar 18, 2026Updated this week
Alternatives and similar repositories for AToM-OpenMM
Users that are interested in AToM-OpenMM are comparing it to the libraries listed below
Sorting:
- The Binding Affinity Tool (BAT.py) is a fully automated tool for absolute binding free energy (ABFE) and relative binding free energy (RB…☆220Mar 4, 2026Updated 2 weeks ago
- Notebooks demonstrating how to do simple tasks related to free energy calculations.☆64Mar 9, 2026Updated last week
- Algorithms for various Network Layouts and Tooling for planning FE Calculations☆22Mar 5, 2026Updated 2 weeks ago
- Open Source, Automated free binding free energy calculation between protein and small molecule. An all-in-one workflow, free energy pertu…☆59Apr 21, 2025Updated 11 months ago
- Cloud-based Drug Binding Structure Prediction☆46Feb 9, 2026Updated last month
- A tutorial for Streamlined Alchemical Free Energy Perturbations with NAMD☆15Mar 11, 2026Updated last week
- Automated Adaptive Absolute alchemical Free Energy calculator☆115Feb 9, 2026Updated last month
- An interoperable Python framework for biomolecular simulation.☆147Updated this week
- A comprehensive toolkit for predicting free energies☆59Jan 10, 2025Updated last year
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆34Dec 10, 2023Updated 2 years ago
- An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.☆200Jul 6, 2023Updated 2 years ago
- An OpenMM plugin that implements the Alchemical Transfer Potential☆40Apr 27, 2023Updated 2 years ago
- Differentiable Markov Chain Monte Carlo☆15Mar 23, 2024Updated last year
- CHARMM and AMBER forcefields for OpenMM (with small molecule support)☆353Mar 4, 2026Updated 2 weeks ago
- the simple alchemistry library☆235Jan 23, 2026Updated last month
- The Open Free Energy toolkit☆262Updated this week
- Fully automated high-throughput MD pipeline☆90Mar 11, 2026Updated last week
- FEP-SPell-ABFE: An Open Source Alchemical Absolute Binding Free Energy Calculation Workflow for Drug Discovery☆83Jan 8, 2025Updated last year
- This package contains tools for setting up hybrid-topology FE calculations☆38Updated this week
- PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods☆207Sep 22, 2023Updated 2 years ago
- This pipeline is executing a RE-EDS run for relative free energy calculations. It can be used for example for calculation of hydration fr…☆33Jun 3, 2025Updated 9 months ago
- Alchemical mutation scoring map☆41Mar 9, 2026Updated last week
- A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.☆316Jan 7, 2026Updated 2 months ago
- Recipes and protocols for molecular free energy calculations using the openmmtools/perses and Open Free Energy toolkits☆16Jan 27, 2026Updated last month
- Package for consistent reporting of relative free energy results☆42Mar 2, 2026Updated 2 weeks ago
- This is a SnakeMake based workflow for ABFE calculations that can be easily scaled in a high-throughput manner via Slurm for example.☆63Dec 17, 2025Updated 3 months ago
- ☆70Jul 19, 2023Updated 2 years ago
- Experiments with expanded ensembles to explore chemical space☆199Oct 28, 2025Updated 4 months ago
- Automated tools for the generation of bespoke SMIRNOFF format parameters for individual molecules.☆74Updated this week
- Data set of protein-ligand complexes with reliable experimental structures and affinities☆44Oct 2, 2025Updated 5 months ago
- BLaDE is a Basic Lambda Dynamics Engine for molecular dynamics based alchemical free energy calculations using multisite lambda dynamics …☆18Sep 16, 2025Updated 6 months ago
- Input files and binding free energy values from our benchmark with QuantumBind-RBFE☆16Apr 16, 2025Updated 11 months ago
- MzDOCK - An Automated GUI based pipeline for Molecular Docking☆26Sep 2, 2025Updated 6 months ago
- A Python module for carrying out GCMC insertions and deletions of water molecules in OpenMM.☆75Jun 12, 2023Updated 2 years ago
- Exploratory work on free energy calculations with GROMACS using "separated topologies" approach (Rocklin et al., 2013).☆28Dec 4, 2024Updated last year
- core data models of the Open Free Energy ecosystem☆40Updated this week
- The OpenMM Cookbook and Tutorials☆56Feb 11, 2026Updated last month
- High level API for using machine learning models in OpenMM simulations☆152Updated this week
- An automatic workflow to perform MM/GB(PB)SA calculations from force field building, and structure optimization to free energy calculatio…☆133Jan 13, 2026Updated 2 months ago