docking Module

The docking module provides utilities for preparing synthetic protein structures for molecular docking simulations and electrostatic calculations.

Overview

Molecular docking requires structures to be in specific formats that include physical parameters beyond simple coordinates. The docking module focuses on converting standard PDB files into PQR format, which includes partial atomic charges and Van der Waals radii.

Key Features

  • PQR Export: Converts PDB files to PQR format using OpenMM for charge assignment.
  • Charge Assignment: Automatically adds missing hydrogens and assigns partial charges based on the AMBER forcefield.
  • Radii Calculation: Derives atomic radii from Lennard-Jones parameters ($\sigma / 2$).
  • PTM Handling: Standardizes non-standard or modified residues for compatibility with standard forcefields.

API Reference

::: synth_pdb.docking handler: python options: members: - DockingPrep

Scientific Principles

The PQR Format

The PQR format is a variation of PDB where: 1. The Occupancy column is replaced by the Partial Charge ($q$) of the atom. 2. The B-factor column is replaced by the Atomic Radius ($r$) in Angstroms.

This format is the standard input for electrostatic solvers like APBS (Adaptive Poisson-Boltzmann Solver) and many docking engines.

Charge Assignment Logic

The module uses OpenMM to: 1. Standardize: Map modified residues (like phosphorylated Serine) to their parent residues if necessary. 2. Protonate: Add hydrogens at a specific pH (default 7.4). 3. Parameterize: Apply a forcefield (default amber14-all.xml) to look up the partial charge for each atom type in its specific chemical environment.

Usage Example

from synth_pdb.docking import DockingPrep

# 1. Initialize the preparation tool
prep = DockingPrep(forcefield_name="amber14-all.xml")

# 2. Convert a synthetic PDB to PQR
# This will add hydrogens and assign charges
success = prep.write_pqr(
    input_pdb="synthetic_protein.pdb", 
    output_pqr="ready_for_docking.pqr"
)

if success:
    print("PQR file created successfully.")