openforcefield / protein-ligand-benchmarkLinks
Protein-Ligand Benchmark Dataset for Free Energy Calculations
☆185Updated 10 months ago
Alternatives and similar repositories for protein-ligand-benchmark
Users that are interested in protein-ligand-benchmark are comparing it to the libraries listed below
Sorting:
- An automated scoring function to facilitate and standardize the evaluation of goal-directed generative models for de novo molecular desig…☆188Updated last month
- Auto3D generates low-energy conformers from SMILES/SDF☆171Updated last month
- The Binding Affinity Tool (BAT.py) is a fully automated tool for absolute binding free energy (ABFE) and relative binding free energy (RB…☆202Updated last week
- Merging, linking and placing compounds by stitching bound compounds together like a reanimated corpse☆188Updated 4 months ago
- Scoring of shape and ESP similarity with RDKit☆218Updated 3 months ago
- A script to run structural alerts using the RDKit and ChEMBL☆144Updated last year
- PINDER: The Protein INteraction Dataset and Evaluation Resource☆125Updated 7 months ago
- A tool for evaluating the predictive performance on activity cliff compounds of machine learning models☆187Updated 4 months ago
- PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods☆190Updated last year
- Multi-domain Distribution Learning for De Novo Drug Design☆90Updated 3 months ago
- PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods☆77Updated 2 years ago
- Tutorials and data necessary to reproduce the results of publication Machine Learning Coarse-Grained Potentials of Protein Thermodynamics☆84Updated 4 months ago
- ☆113Updated 10 months ago
- Benchmark set for relative free energy calculations.☆107Updated last year
- An Open-Source Molecular Builder and Free Energy Preparation Workflow☆124Updated 3 months ago
- BitBIRCH clustering algorithm☆83Updated 3 weeks ago
- Comprehensive benchmarking of protein-ligand structure prediction methods. (ICML 2024 AI4Science)☆158Updated 2 months ago
- An interoperable Python framework for biomolecular simulation.☆115Updated this week
- Toolkit for free-energy calculation setup/analysis and biomolecular structure handling☆150Updated last month
- The official repository of Uni-pKa☆62Updated 2 months ago
- OpenMM-based framework for absolute and relative binding free energy calculations with the Alchemical Transfer Method☆134Updated last week
- An automatic workflow to perform MM/GB(PB)SA calculations from force field building, and structure optimization to free energy calculatio…☆112Updated 7 months ago
- DockStream: A Docking Wrapper to Enhance De Novo Molecular Design☆119Updated 2 years ago
- A geometric flow matching model for generative protein-ligand docking and affinity prediction. (ISMB 2025)☆93Updated 2 months ago
- Diffusion model based protein-ligand flexible docking method☆106Updated 7 months ago
- Protein Ligand INteraction Dataset and Evaluation Resource☆229Updated last week
- Implementations of different GNNs from scratch for chemists☆138Updated last month
- Trained caffe models☆91Updated last year
- Interface to OpenMM for easy setup of molecular dynamic simulations of protein-ligand complexes☆135Updated this week
- Extensible Surrogate Potential of Ab initio Learned and Optimized by Message-passing Algorithm 🍹https://arxiv.org/abs/2010.01196☆238Updated 2 weeks ago