Gallicchio-Lab / AToM-OpenMM
OpenMM-based framework for absolute and relative binding free energy calculations with the Alchemical Transfer Method
☆132Updated last month
Alternatives and similar repositories for AToM-OpenMM:
Users that are interested in AToM-OpenMM are comparing it to the libraries listed below
- An Open-Source Molecular Builder and Free Energy Preparation Workflow☆123Updated last month
- Toolkit for free-energy calculation setup/analysis and biomolecular structure handling☆143Updated 3 weeks ago
- OpenMM plugin to interface with PLUMED☆66Updated 2 months ago
- Automated tools for the generation of bespoke SMIRNOFF format parameters for individual molecules.☆67Updated this week
- Force fields produced by the Open Force Field Initiative☆149Updated 2 weeks ago
- Describe and apply transformation on molecular structures and topologies☆112Updated this week
- the simple alchemistry library☆213Updated 4 months ago
- A Python module for carrying out GCMC insertions and deletions of water molecules in OpenMM.☆67Updated last year
- Benchmark set for relative free energy calculations.☆105Updated 11 months ago
- ☆64Updated last year
- Protein-Ligand Benchmark Dataset for Free Energy Calculations☆173Updated 9 months ago
- ☆54Updated 2 years ago
- binding free energy estimator 2☆113Updated last week
- 📐 Symmetry-corrected RMSD in Python☆97Updated last week
- PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods☆75Updated last year
- Martini 3 small-molecule database☆59Updated 8 months ago
- Tutorial on the setup and simulation of a membrane protein with AMBER Lipid21 and PACKMOL-Memgen☆62Updated last year
- A python toolkit for analysing membrane protein-lipid interactions.☆63Updated 2 years ago
- Best practice document for alchemical free energy calculations going to livecoms journal☆71Updated 2 months ago
- Enable cheminformatics and quantum chemistry☆74Updated last year
- Scoring of shape and ESP similarity with RDKit☆214Updated last month
- Gaussian Accelerated Molecular Dynamics (GaMD) is a computational method for both unconstrained enhanced sampling and free energy calcula…☆81Updated last week
- Interface to OpenMM for easy setup of molecular dynamic simulations of protein-ligand complexes☆127Updated this week
- The Binding Affinity Tool (BAT.py) is a fully automated tool for absolute binding free energy (ABFE) and relative binding free energy (RB…☆197Updated 2 months ago
- A comprehensive toolkit for predicting free energies☆52Updated 3 months ago
- Automated Adaptive Absolute alchemical Free Energy calculator☆92Updated last week
- The Chemical Data Processing Toolkit☆86Updated this week
- Auto3D generates low-energy conformers from SMILES/SDF☆167Updated last month
- ☆124Updated last year
- An interoperable Python framework for biomolecular simulation.☆109Updated last month