openforcefield / protein-ligand-benchmarkLinks
Protein-Ligand Benchmark Dataset for Free Energy Calculations
☆187Updated 11 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:
- The Binding Affinity Tool (BAT.py) is a fully automated tool for absolute binding free energy (ABFE) and relative binding free energy (RB…☆204Updated last month
- Auto3D generates low-energy conformers from SMILES/SDF☆172Updated last month
- Merging, linking and placing compounds by stitching bound compounds together like a reanimated corpse☆189Updated 5 months ago
- An automated scoring function to facilitate and standardize the evaluation of goal-directed generative models for de novo molecular desig…☆191Updated this week
- Scoring of shape and ESP similarity with RDKit☆221Updated 3 months ago
- A script to run structural alerts using the RDKit and ChEMBL☆145Updated last year
- An interoperable Python framework for biomolecular simulation.☆118Updated this week
- Reduce - tool for adding and correcting hydrogens in PDB files☆147Updated last month
- PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods☆190Updated last year
- An automatic workflow to perform MM/GB(PB)SA calculations from force field building, and structure optimization to free energy calculatio…☆112Updated 8 months ago
- A Python package for molecular docking with an extensive, highly-curated dataset and a set of realistic benchmark tasks for drug discover…☆172Updated 2 months ago
- PENSA - a collection of python methods for exploratory analysis and comparison of biomolecular conformational ensembles.☆140Updated 5 months ago
- CReM: chemically reasonable mutations framework☆237Updated 3 weeks ago
- Benchmark set for relative free energy calculations.☆110Updated last year
- An Open-Source Molecular Builder and Free Energy Preparation Workflow☆125Updated this week
- BitBIRCH clustering algorithm☆89Updated last month
- Simple protein-ligand complex simulation with OpenMM☆85Updated last year
- A Python package for processing molecules with RDKit in scikit-learn☆198Updated this week
- Toolkit for free-energy calculation setup/analysis and biomolecular structure handling☆151Updated this week
- Tutorials and data necessary to reproduce the results of publication Machine Learning Coarse-Grained Potentials of Protein Thermodynamics☆85Updated 5 months ago
- Multi-domain Distribution Learning for De Novo Drug Design☆97Updated 3 months ago
- PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods☆77Updated 2 years ago
- A package to identify matched molecular pairs and use them to predict property changes.☆237Updated last month
- A tool for evaluating the predictive performance on activity cliff compounds of machine learning models☆187Updated 4 months ago
- PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.☆150Updated 4 months ago
- Code related to : O. Mendez-Lucio, M. Ahmad, E.A. del Rio-Chanona, J.K. Wegner, A Geometric Deep Learning Approach to Predict Binding Co…☆179Updated 3 years ago
- The public versio☆59Updated 2 years ago
- A Graph-Convolutional Deep Neural Network for predicting electrostatic potential surfaces☆90Updated 2 years ago
- Protein Ligand INteraction Dataset and Evaluation Resource☆233Updated last month
- OpenMM-based framework for absolute and relative binding free energy calculations with the Alchemical Transfer Method☆135Updated 2 weeks ago