This library implements a web based GUI to DeepChem. As of present, it can be used to predict docking of ligands to proteins using DeepChem models pretrained on PDBBind. The GUI heavily relies on the molecular visualization library NGL, and is modeled after its demo web application.
Installation from source is the only currently supported format.
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Install DeepChem using the instructions here.
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Install Flask: In the Anaconda environment you created in the previous step to install DeepChem, execute-
pip install Flask
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Clone the
deepchem-gui
github repo:git clone https://github.com/deepchem/deepchem-gui.git
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Launch the web application:
At present, the only way to access the GUI is to run the server on your local machine. In the Anaconda environment with DeepChem installed,cd
into thedeepchem-gui
directory and execute-export FLASK_APP=deepchem-gui.py flask run
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Navigate to http://127.0.0.1:5000/ in your browser to open the application.
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Select a ligand file and a protein file using the file selection tool in Dock tab. At present, the only supported format for ligand files is .sdf and for protein files is .pdb
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Docking takes approx. 5 minutes, following which the predicted score and poses for the ligand are displayed in the browser.
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Update the molecular visualizations using the options in the right panel as specified in these instructions.
Note: This repository is under active development so bugs and surprises are likely. Kindly raise an issue on GitHub if you run into problems and we will try and resolve it asap. Alternatively you can also contribute to the repository by following these guidelines. Client side issues can be inspected using the JavaScript console of the browser while server side errors will be displayed in the shell.
- Computational Modeling of β-secretase 1 (BACE-1) Inhibitors using Ligand Based Approaches
- Low Data Drug Discovery with One-shot Learning
DeepChem is a package by the Pande group at Stanford. DeepChem was originally created by Bharath Ramsundar, and has grown through the contributions of a number of undergraduate, graduate, and postdoctoral researchers working with the Pande lab.