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An automated drug discovery pipeline

Project description

SieveAI

An automated drug discovery pipeline

Features

  • Automated blind docking and rescoring
  • Automated result parsing and aggregation
  • Basic version for AutoDock VINA 1.2.3
  • Customisable to include local, api, or web based tools

Quick installation and usage

  • pip install SieveAI
  • sieveai -h

Installing basic requirements for basic docking

Requirements for AutoDock VINA

  1. Python

    • Download and install python
    • Preferred versions 3.8 - 3.10
  2. SieveAI > 0.4 pip install sieveai

  3. AutoDock VINA 1.2.3

  • Step 1: Navigate to vina binary on GitHub
  • Ubuntu 20 LTS
    • Step 2: Download vina_1.2.3_linux_x86_64 (for Linux)
    • Step 3: Rename downloaded file to vina and move to /opt/AutoDock/ in Ubuntu
  • Windows
    • Step 2: Download vina_1.2.3_windows_x86_64.exe (for windows)
    • Step 3: Rename downloaded file to vina and move it program directory. Add directory to environmental variables.
  1. AutoDock Tools/MGL Tools
  • Download ADFR Suit for Linux/Windows and install as per given instructions
  • Add executable path to bashrc in Ubuntu or add directory to environmental variables in Windows

Make sure that vina, prepare_ligand, mk_prepare_ligand and prepare_receptor commands available through commandline

  1. ChimeraX
  • Step 1: Download Chimerax from download page
  • Step 2: sudo apt-get install ./ucsf-chimerax_1.3ubuntu20.04_amd64.deb
  • Confirm ChimeraX availble through commandline chimerax
  1. Openbabel (Optional)
  • Ubuntu 20 LTS
    • STEP 1: sudo apt-get install openbabel
    • Confirm OpenBabel availble through commandline obabel
  • Windows
    • Get OpenBabel download from here
    • Add obabel path to environment PATH variables
  1. FreeSASA (Optional)

0.5.20230606

  • Bug Fixes

0.1.20210630

  • Version 0.1

Copyright

© Vishal Kumar Sahu, 2023

Project details


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SieveAI-0.6.20231212.tar.gz (28.7 kB view hashes)

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