choderalab / yankLinks
An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.
☆193Updated 2 years ago
Alternatives and similar repositories for yank
Users that are interested in yank are comparing it to the libraries listed below
Sorting:
- the simple alchemistry library☆232Updated last week
- Python implementation of the multistate Bennett acceptance ratio (MBAR)☆291Updated 3 months ago
- Describe and apply transformation on molecular structures and topologies☆135Updated 2 weeks ago
- A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.☆313Updated 3 weeks ago
- Experiments with expanded ensembles to explore chemical space☆199Updated 3 months ago
- Force fields produced by the Open Force Field Initiative☆175Updated 3 weeks ago
- A document for the Living Journal of Computational Molecular Science (LiveCoMS) which describes basic training for molecular simulations …☆117Updated 7 years ago
- Toolkit for free-energy calculation setup/analysis and biomolecular structure handling☆167Updated last week
- OpenMM-based framework for absolute and relative binding free energy calculations with the Alchemical Transfer Method☆151Updated 2 weeks ago
- CHARMM and AMBER forcefields for OpenMM (with small molecule support)☆346Updated 3 weeks ago
- Experimental and calculated small molecule hydration free energies☆132Updated 3 years ago
- OpenMM plugin to define forces with neural networks☆220Updated 11 months ago
- GromacsWrapper wraps system calls to GROMACS tools into thin Python classes (GROMACS 4.6.5 - 2024 supported).☆185Updated 5 months ago
- HTMD: Programming Environment for Molecular Discovery☆272Updated 2 months ago
- The Open Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools. Documentation avai…☆379Updated 2 weeks ago
- An interoperable Python framework for biomolecular simulation.☆143Updated last week
- An open tool implementing some recommended practices for analyzing alchemical free energy calculations☆135Updated last year
- Extensible Surrogate Potential of Ab initio Learned and Optimized by Message-passing Algorithm 🍹https://arxiv.org/abs/2010.01196☆262Updated 7 months ago
- High level API for using machine learning models in OpenMM simulations☆141Updated last week
- PROPKA predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure.☆333Updated last week
- LOOS: a lightweight object-oriented structure analysis library☆127Updated 3 months ago
- Benchmark set for relative free energy calculations.☆118Updated last year
- WESTPA: The Weighted Ensemble Simulation Toolkit with Parallelization and Analysis☆209Updated 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…☆219Updated last week
- OpenMM plugin to interface with PLUMED☆74Updated 3 weeks ago
- MoleculeKit: Your favorite molecule manipulation kit☆232Updated last month
- Python interface of cpptraj☆186Updated 2 weeks ago
- Auto3D generates low-energy conformers from SMILES/SDF