Please note: this repository is no longer being maintained.

DockStreamCommunity

Description

This repository is meant to store Jupyter Notebook tutorials and documentation for DockStream.

Supported Backends

Ligand Embedders

• RDKit
• Corina
• OpenEye's OMEGA
• Schrodinger's LigPrep
• TautEnum

Docking Backends

• AutoDock Vina
• rDock
• OpenEye's Hybrid
• Schrodinger's Glide
• CCDC's GOLD

Note, that the CCDC package, the OpenEye toolkit and Schrodinger's tools require you to obtain the respective software from those vendors.

Using DockStream in REINVENT

DockStream provides a flexible implementation of molecular docking as a scoring function component in REINVENT. The generative agent is able to gradually generate compounds that satisfy the DockStream component, i.e, achieve favourable docking scores. A tutorial notebook is provided.

Requirements

A Conda environment is provided: DockStreamCommunity via environment.yml to execute the Jupyter Notebook tutorials. Some notebooks also require the DockStream and DockStreamFull environments to be installed (see DockStream README).

git clone <DockStreamCommunity repository>
cd <DockStreamCommunity directory>
conda env create -f environment.yml
conda activate DockStreamCommunity
jupyter notebook

Contributors

Christian Margreitter ([email protected]) Jeff Guo ([email protected]) Alexey Voronov ([email protected])