irrelevant2021's repositories
perses
Experiments with expanded ensembles to explore chemical space
alphafold
Open source code for AlphaFold.
regression-transformer
Regression Transformer (2023; Nature Machine Intelligence)
making-it-rain
Cloud-based molecular simulations for everyone
NamdFEP
easy to start a FEP
AMBER-Maestro-lipid-tutorial
Tutorial to build AMBER compatable protein+lipid systems
gnina
A deep learning framework for molecular docking
openmmforcefields
CHARMM and AMBER forcefields for OpenMM (with small molecule support)
AToM-OpenMM
OpenMM-based framework for absolute and relative binding free energy calculations with the Alchemical Transfer Method
EquiBind
EquiBind: geometric deep learning for fast predictions of the 3D structure in which a small molecule binds to a protein
NAMD-FEP
You should run this on a computer station or cluster. Calculate the binding free energy difference between two small molecules against the same protein target.
BAT.py
The Binding Affinity Tool (BAT.py) is a fully automated tool for absolute binding free energy calculations on protein-ligand systems.
Jupyter_Dock
Jupyter Dock is a set of Jupyter Notebooks for performing molecular docking protocols interactively, as well as visualizing, converting file formats and analyzing the results.
gmx_MMPBSA
gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.
crest
Conformer-Rotamer Ensemble Sampling Tool based on the xtb Semiempirical Extended Tight-Binding Program Package
chembl_webresource_client
Official Python client for accessing ChEMBL API.
MDNotebooks
Jupyter Notebooks for Molecular Dynamics
fep-benchmark
Benchmark set for relative free energy calculations.
masif
MaSIF- Molecular surface interaction fingerprints. Geometric deep learning to decipher patterns in molecular surfaces.
drugbank
User-friendly extensions of the DrugBank database