OpenMM-based framework for absolute and relative binding free energy calculations with the Alchemical Transfer Method
☆154Updated 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…☆220Jan 27, 2026Updated last month
- Notebooks demonstrating how to do simple tasks related to free energy calculations.☆64Feb 9, 2026Updated 3 weeks ago
- Algorithms for various Network Layouts and Tooling for planning FE Calculations☆20Feb 20, 2026Updated last week
- An interoperable Python framework for biomolecular simulation.☆146Updated this week
- Automated Adaptive Absolute alchemical Free Energy calculator☆114Feb 9, 2026Updated 3 weeks ago
- A tutorial for Streamlined Alchemical Free Energy Perturbations with NAMD☆15Mar 20, 2025Updated 11 months ago
- Cloud-based Drug Binding Structure Prediction☆46Feb 9, 2026Updated 3 weeks ago
- The Open Free Energy toolkit☆253Feb 23, 2026Updated last week
- Fully automated high-throughput MD pipeline☆89Feb 13, 2026Updated 2 weeks ago
- CHARMM and AMBER forcefields for OpenMM (with small molecule support)☆350Jan 6, 2026Updated last month
- 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.☆193Jul 6, 2023Updated 2 years ago
- FEP-SPell-ABFE: An Open Source Alchemical Absolute Binding Free Energy Calculation Workflow for Drug Discovery☆83Jan 8, 2025Updated last year
- Differentiable Markov Chain Monte Carlo☆15Mar 23, 2024Updated last year
- Open Source, Automated free binding free energy calculation between protein and small molecule. An all-in-one workflow, free energy pertu…☆59Apr 21, 2025Updated 10 months ago
- the simple alchemistry library☆234Jan 23, 2026Updated last month
- A comprehensive toolkit for predicting free energies☆58Jan 10, 2025Updated last year
- PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods☆206Sep 22, 2023Updated 2 years ago
- A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.☆315Jan 7, 2026Updated last month
- Automated tools for the generation of bespoke SMIRNOFF format parameters for individual molecules.☆72Feb 13, 2026Updated 2 weeks ago
- The OpenMM Cookbook and Tutorials☆56Feb 11, 2026Updated 2 weeks 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…☆32Jun 3, 2025Updated 8 months ago
- An OpenMM plugin that implements the Alchemical Transfer Potential☆40Apr 27, 2023Updated 2 years ago
- This is a SnakeMake based workflow for ABFE calculations that can be easily scaled in a high-throughput manner via Slurm for example.☆61Dec 17, 2025Updated 2 months ago
- Protein-Ligand Benchmark Dataset for Free Energy Calculations☆216Jul 29, 2024Updated last year
- Recipes and protocols for molecular free energy calculations using the openmmtools/perses and Open Free Energy toolkits☆16Jan 27, 2026Updated last month
- A tutorials suite for BioSimSpace.☆34Oct 22, 2025Updated 4 months ago
- Sire Molecular Simulations Framework☆64Feb 18, 2026Updated last week
- Input files and binding free energy values from our benchmark with QuantumBind-RBFE☆16Apr 16, 2025Updated 10 months ago
- SubPEx (Sub-Pocket Explorer) is a tool to enhance ensemble (multiple-receptor/relaxed-complex) virtual screening. It uses weighted ensemb…☆18Jun 30, 2025Updated 8 months ago
- ☆70Jul 19, 2023Updated 2 years ago
- An Open-Source Molecular Builder and Free Energy Preparation Workflow☆140Nov 10, 2025Updated 3 months ago
- High level API for using machine learning models in OpenMM simulations☆149Feb 20, 2026Updated last week
- This package contains tools for setting up hybrid-topology FE calculations☆38Feb 20, 2026Updated last week
- core data models of the Open Free Energy ecosystem☆40Updated this week
- Alchemical mutation scoring map☆41Nov 21, 2025Updated 3 months ago
- Python implementation of the multistate Bennett acceptance ratio (MBAR)☆292Feb 12, 2026Updated 2 weeks ago
- Experiments with expanded ensembles to explore chemical space☆199Oct 28, 2025Updated 4 months ago
- Interaction Fingerprints for protein-ligand complexes and more☆477Feb 22, 2026Updated last week