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alphafold

Open source code for AlphaFold.

amber-maestro-lipid-tutorial

Tutorial to build AMBER compatable protein+lipid systems

atom-openmm

OpenMM-based framework for absolute and relative binding free energy calculations with the Alchemical Transfer Method

bat.py

The Binding Affinity Tool (BAT.py) is a fully automated tool for absolute binding free energy calculations on protein-ligand systems.

chembl_webresource_client

Official Python client for accessing ChEMBL API.

crest

Conformer-Rotamer Ensemble Sampling Tool based on the xtb Semiempirical Extended Tight-Binding Program Package

drugbank

User-friendly extensions of the DrugBank database

equibind

EquiBind: geometric deep learning for fast predictions of the 3D structure in which a small molecule binds to a protein

fep-benchmark

Benchmark set for relative free energy calculations.

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.

gnina

A deep learning framework for molecular docking

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.

making-it-rain

Cloud-based molecular simulations for everyone

masif

MaSIF- Molecular surface interaction fingerprints. Geometric deep learning to decipher patterns in molecular surfaces.

mdnotebooks

Jupyter Notebooks for Molecular Dynamics

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.

namd-md

namdfep

easy to start a FEP

openmmforcefields

CHARMM and AMBER forcefields for OpenMM (with small molecule support)

perses

Experiments with expanded ensembles to explore chemical space

regression-transformer

Regression Transformer (2023; Nature Machine Intelligence)