choderalab / persesLinks
Experiments with expanded ensembles to explore chemical space
☆192Updated 6 months ago
Alternatives and similar repositories for perses
Users that are interested in perses are comparing it to the libraries listed below
Sorting:
- An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.☆186Updated 2 years ago
- Python implementation of the multistate Bennett acceptance ratio (MBAR)☆264Updated 3 weeks ago
- The Open Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools. Documentation avai…☆350Updated last week
- WESTPA: The Weighted Ensemble Simulation Toolkit with Parallelization and Analysis☆203Updated last week
- the simple alchemistry library☆219Updated last month
- Extensible Surrogate Potential of Ab initio Learned and Optimized by Message-passing Algorithm 🍹https://arxiv.org/abs/2010.01196☆241Updated last month
- A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.☆284Updated this week
- High level API for using machine learning models in OpenMM simulations☆119Updated last month
- Force fields produced by the Open Force Field Initiative☆155Updated last month
- CHARMM and AMBER forcefields for OpenMM (with small molecule support)☆314Updated last week
- Systematic force field optimization.☆151Updated 8 months ago
- OpenMM plugin to define forces with neural networks☆201Updated 5 months ago
- HTMD: Programming Environment for Molecular Discovery☆267Updated last month
- Experimental and calculated small molecule hydration free energies☆120Updated 2 years ago
- An interoperable Python framework for biomolecular simulation.☆119Updated this week
- Describe and apply transformation on molecular structures and topologies☆118Updated this week
- Tinker: Software Tools for Molecular Design☆144Updated last week
- A Python library which allows construction and manipulation of complex molecules, as well as automatic molecular design and the creation …☆267Updated 3 weeks ago
- Converts an xyz file to an RDKit mol object☆271Updated 6 months ago
- OpenMM-based framework for absolute and relative binding free energy calculations with the Alchemical Transfer Method☆135Updated last month
- A document for the Living Journal of Computational Molecular Science (LiveCoMS) which describes basic training for molecular simulations …☆115Updated 6 years ago
- psi4+RDKit☆101Updated 2 months ago
- Protein-Ligand Benchmark Dataset for Free Energy Calculations☆190Updated last year
- An open source Python framework for transition interface and path sampling calculations.☆112Updated 2 months ago
- ANI-1 neural net potential with python interface (ASE)☆223Updated last year
- An open tool implementing some recommended practices for analyzing alchemical free energy calculations☆129Updated last year
- The Binding Affinity Tool (BAT.py) is a fully automated tool for absolute binding free energy (ABFE) and relative binding free energy (RB…☆207Updated this week
- OpenMM plugin to interface with PLUMED☆68Updated 5 months ago
- A script to run structural alerts using the RDKit and ChEMBL☆145Updated 2 years ago
- The Open Free Energy toolkit☆190Updated last week