choderalab / persesLinks
Experiments with expanded ensembles to explore chemical space
β192Updated 4 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.β186Updated last year
- Extensible Surrogate Potential of Ab initio Learned and Optimized by Message-passing Algorithm πΉhttps://arxiv.org/abs/2010.01196β239Updated this week
- the simple alchemistry libraryβ215Updated 3 weeks ago
- A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.β278Updated 2 weeks ago
- The Open Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools. Documentation avaiβ¦β340Updated 2 weeks ago
- CHARMM and AMBER forcefields for OpenMM (with small molecule support)β300Updated last month
- Python implementation of the multistate Bennett acceptance ratio (MBAR)β257Updated 2 months ago
- OpenMM plugin to define forces with neural networksβ199Updated 3 months ago
- High level API for using machine learning models in OpenMM simulationsβ109Updated 2 months ago
- Systematic force field optimization.β151Updated 6 months ago
- Force fields produced by the Open Force Field Initiativeβ151Updated last month
- CReM: chemically reasonable mutations frameworkβ234Updated last week
- Atoms In Molecules Neural Network Potentialβ105Updated 5 years ago
- The Binding Affinity Tool (BAT.py) is a fully automated tool for absolute binding free energy (ABFE) and relative binding free energy (RBβ¦β199Updated 3 months ago
- A script to run structural alerts using the RDKit and ChEMBLβ143Updated last year
- MoleculeKit: Your favorite molecule manipulation kitβ220Updated this week
- Describe and apply transformation on molecular structures and topologiesβ113Updated 2 weeks ago
- Auto3D generates low-energy conformers from SMILES/SDFβ171Updated 2 weeks ago
- An interoperable Python framework for biomolecular simulation.β115Updated this week
- An open tool implementing some recommended practices for analyzing alchemical free energy calculationsβ128Updated last year
- Converts an xyz file to an RDKit mol objectβ271Updated 4 months ago
- WESTPA: The Weighted Ensemble Simulation Toolkit with Parallelization and Analysisβ201Updated last week
- Protein-Ligand Benchmark Dataset for Free Energy Calculationsβ179Updated 10 months ago
- Merging, linking and placing compounds by stitching bound compounds together like a reanimated corpseβ188Updated 4 months ago
- ScaffoldGraph is an open-source cheminformatics library, built using RDKit and NetworkX, for the generation and analysis of scaffold netwβ¦β181Updated 3 years ago
- Interaction Fingerprints for protein-ligand complexes and moreβ416Updated last week
- A document for the Living Journal of Computational Molecular Science (LiveCoMS) which describes basic training for molecular simulations β¦β114Updated 6 years ago
- Scoring of shape and ESP similarity with RDKitβ216Updated 2 months ago
- OpenMM-based framework for absolute and relative binding free energy calculations with the Alchemical Transfer Methodβ134Updated this week
- Some useful RDKit functionsβ183Updated 3 weeks ago