Quick start¶

What is ProtacTM?¶

ProtacTM is a package designed for PROTAC ternary complex modeling. It can model the formation of Target-PROTAC-E3 complex structures using Target-Ligand and E3-Ligand complexes along with PROTAC SMILES.

As a python package, it provides object-oriented APIs for analyzing and manipulating PROTACs and their ternary complexes, while also encapsulating commonly used methods in PROTAC ternary complex modeling workflows to facilitate new protocol development.

Installation¶

You can install protactm package directly using pip in a Python 3.8 environment:

pip install protactm

For better package management and to avoid potential conflicts with other Python packages, we recommend using a Python environment manager, you can learn more about venv or Conda.

Dependencies¶

The protactm module requires Schrodinger software installation:

Schrodinger Suite can be installed from Schrodinger Official Website. A valid license is required for specific functionalities.

For academic institutions:

Desmond (with bundled Maestro). You can apply for a download link form De Shaw Research Group Website.
Maestro Viewer. You can download from Schrodinger Official Website.

When using protactm package with Schrodinger, you must comply with Schrodinger's End User License Agreement (EULA).

The protactm package has been verified to be compatible with Schrodinger versions 2022-4 through 2023-4. For issues with other versions, please report at GitHub Issues.

Examples¶

from protactm.sch import ProtacAtoms, Structure

# Read PROTAC molecule from structure file
protac = ProtacAtoms.read_first("protac.mae")

# Automatically identify linker part
print(protac.linker.smarts)

# Identify linker from protein-ligand complexes
complexes = [
    Structure.read_first("target_ligand.mae"),
    Structure.read_first("e3_ligand.mae")
]
linker = protac.guess_linker_from(complexes)