mirastic / sieveai-dev

An automated drug discovery pipeline

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.

4. 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

5. 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

6. 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

7. FreeSASA (Optional)

• Follow instructions at https://freesasa.github.io/
• Download https://freesasa.github.io/freesasa-2.0.3.tar.gz and extract

• ./configure
  make
  sudo make install
  freesasa -h```
  

0.5.20230606

• Bug Fixes

0.1.20210630

• Version 0.1

Copyright

© Vishal Kumar Sahu, 2023