Drug Sniffer

Drug Sniffer is a virtual screening (VS) pipeline capable of screening billions of molecules using only thousands of CPU hours, using a novel combination of ligand-based (LBVS) and structure-based (SBVS) methods.

The pipeline requires the user to identify the structure and pocket of the target protein (stages 1 and 2). These stages are completed manually by the user.

Then, the pipeline begins by designing multiple de novo ligands for the identified binding pockets (stage 3). Next, it uses these ligands as seeds to identify similar compounds from a small-molecule database (stage 4). The resulting neighbors are then subjected to rigid-body docking (stage 5) and re-ranked with a new scoring model (stage 6).

Optionally, the pipeline also allows the user to run possible ligands through FP-ADMET, an ADMET filter (stage 7).

The Drug Sniffer pipeline has been implemented as a Nextflow workflow. Each stage has a corresponding script and Docker image that are used to execute the computations contained in the stage.

Documentation

The project documentation can be found at http://drugsniffer.org.

About the Repo

End-to-end tests and associated data are stored in test/. The workflow itself, implemented using Nextflow, can be found in workflow/.

The site/ directory contains the project web site source code. The HTML and other assorted files live in the docs/ directory where they can be served by GitHub Pages.

Contributing

Contributions are welcome. Fork this repository, modify the contents, and then create a pull request. Someone will look over it and provide feedback, then merge it when it is ready.

License

Original code and configuration are under the BSD 3-clause license. Third-party software is licensed separately.