choderalab / espaloma
Extensible Surrogate Potential of Ab initio Learned and Optimized by Message-passing Algorithm πΉhttps://arxiv.org/abs/2010.01196
β222Updated 2 months ago
Alternatives and similar repositories for espaloma:
Users that are interested in espaloma are comparing it to the libraries listed below
- CReM: chemically reasonable mutations frameworkβ214Updated last month
- Auto3D generates low-energy conformers from SMILES/SDFβ154Updated 5 months ago
- Protein-Ligand Benchmark Dataset for Free Energy Calculationsβ161Updated 6 months ago
- Force fields produced by the Open Force Field Initiativeβ143Updated 3 weeks ago
- OpenMM plugin to define forces with neural networksβ190Updated 2 months ago
- CHARMM and AMBER forcefields for OpenMM (with small molecule support)β271Updated 3 weeks ago
- the simple alchemistry libraryβ204Updated last month
- A script to run structural alerts using the RDKit and ChEMBLβ135Updated last year
- A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.β257Updated this week
- The Binding Affinity Tool (BAT.py) is a fully automated tool for absolute binding free energy (ABFE) and relative binding free energy (RBβ¦β185Updated this week
- An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.β183Updated last year
- Scoring of shape and ESP similarity with RDKitβ208Updated last year
- OpenMM-based framework for absolute and relative binding free energy calculations with the Alchemical Transfer Methodβ126Updated last week
- The Open Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools. Documentation avaiβ¦β325Updated this week
- Converts an xyz file to an RDKit mol objectβ256Updated last week
- Interaction Fingerprints for protein-ligand complexes and moreβ380Updated last week
- active learning for accelerated high-throughput virtual screeningβ172Updated 7 months ago
- Python implementation of the multistate Bennett acceptance ratio (MBAR)β243Updated 4 months ago
- A collection of QM data for training potential functionsβ160Updated last week
- Plausibility checks for generated molecule poses.β245Updated this week
- Merging, linking and placing compounds by stitching bound compounds together like a reanimated corpseβ180Updated this week
- PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methodsβ173Updated last year
- Some useful RDKit functionsβ153Updated last month
- PROPKA predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure.β276Updated 11 months ago
- This repository contains code for the paper: Beyond Generative Models: Superfast Traversal, Optimization, Novelty, Exploration and Discovβ¦β123Updated 5 months ago
- OpenMM tutorial for the MSBS courseβ156Updated this week
- Atoms In Molecules Neural Network Potentialβ102Updated 5 years ago
- Molecule Validation and Standardizationβ166Updated 4 years ago
- MoleculeKit: Your favorite molecule manipulation kitβ209Updated this week
- β123Updated 9 months ago