struct2block 1.1

Detect functional block of protein. If you have two different proteins that bind to the same target protein. Struct2Block is an easy tool designed for quickly evaluating the following situations:1) An antibody binds to a receptor. To what extent does it sterically hinder the ligand. 2)2 different ligands bind to the same receptor. To what degree does they compete.

Struct2Block

Detect functional blocking.

If you have two different proteins that bind to the same target protein. Struct2Block is an easy tool designed for quickly evaluating the following situations:

• An antibody binds to a receptor. To what extent does it sterically hinder the ligand.
• 2 different ligands bind to the same receptor. To what degree does they compete.

1 Install

1.1 pip

pip install struct2block

1.2 conda

conda install chou_uken::struct2block
mamba install chou_uken::struct2block

2 How to use

2.1 As a Command Line Application

To get usage instructions.

struct2block --help

For example, you can use this command line:

struct2block A.pdb B.pdb

It will use A.pdb as antigen-ligand complex and B.pdb as Antibody-antigen complex. Then some details and results will be printed in the console. If you don't need any output, use option -q or --quiet. You can also output superimposed structures with following command line.

struct2block A.pdb B.pdb prefix

Then your structures will be output as prefix_antibody.pdb and prefix_ligand.pdb.

2.2 As a Python API

def struct2block(complex: str, anti: str, prefix: str=None, quiet: bool=False) -> float:
    """Calculate the steric clash volume (block rate) of antibody.
    Block rate = Volume of ligand occupied by antibody / Total volume of ligand
    
    Args:
        complex (str): PDB file containing Antigen-Ligand model.
        anti (str): PDB file containing Antigen-Antibody model.
        prefix (str): The file prefix you want to store the superimposed complex structures.
        quiet (bool): If true, suppress the output.

    Returns:
        blockRate (float): block rate.
    """

For example:

from struct2block.struct2block import struct2block
br: float = struct2block(complex="antigen-ligand.pdb", anti="antigen-antibody.pdb", quiet=False)

3 How does it work

First, Struct2Block find the most similar shared chain in two PDB files as antigen. Then it calculates the space (V_ligand) occupied by the ligand in the antigen-ligand complex. Next, it calculates the volume of that same space that is now occupied by the antibody in the antigen-antibody complex (V_antibody ∩ ligand). Then the steric clash volume of ligand (called 'block rate')

block rate = V(antibody ∩ ligand) / V(ligand)