Welcome to asapdiscovery’s documentation!

All pandemics are global health threats. Our best defense is a healthy global antiviral discovery community with a robust pipeline of open discovery tools. The AI-driven Structure-enabled Antiviral Platform is making this a reality!

The toolkit in this repo is a batteries-included drug discovery pipeline being actively developed in a transparent open-source way, with a focus on computational chemistry and informatics support for medicinal chemistry. Coupled with ASAP’s active data disclosures our campaign to develop a new series of antivirals can provide insight into the drug discovery process that is normally conducted behind closed doors.

Note

asapdiscovery is not designed as a one size fits all solution for drug discovery, rather it is our opinionated tooling designed with our targets in mind. Your mileage will vary if not using an ASAP target.

The asapdiscovery toolkit is focused around the following core competencies, organised into submodules:

  • asapdiscovery-alchemy: Free energy calculations using OpenFE and Alchemiscale

  • asapdiscovery-cli: Command line tools uniting the whole repo.

  • asapdiscovery-data: Core data models and integrations with services such as postera.ai , Collaborative Drug Discovery Vault`, and Diamond Light Source’s Fragalysis database

  • asapdiscovery-dataviz: Data and structure visualization using 3DMol and PyMOL

  • asapdiscovery-docking: Docking and compound screening with the OpenEye toolkit

  • asapdiscovery-genetics: Working with sequence and fitness information and conducting protein structure inference

  • asapdiscovery-ml: Structure and graph based ML models for predicting compound activity and other endpoints

  • asapdiscovery-modelling: Structure prep and standardisation

  • asapdiscovery-simulation: MD simulations and analysis using OpenMM

  • asapdiscovery-workflows: Workflows that combine components to enable end to end project support

The asapdiscovery toolkit is currently focused on ASAP’s targets, which are enumerated on the ASAP website.

See future for more information on our roadmap and future plans for the toolkit.

Disclaimer

asapdiscovery is pre-alpha and is under very active development, we make no guarantees around correctness and the API is liable to change rapidly at any time.