PDB2PQR

PDB2PQR converts Protein Data Bank (PDB) files into PQR format to prepare biomolecular structures for electrostatics calculations and related biophysical analyses.

Key Features:

• Atom Addition and Optimization: Adds missing heavy atoms to biomolecular structures to produce complete coordinate sets.
• Hydrogen Bonding Optimization: Optimizes hydrogen bonding configurations to improve modeling of molecular interactions and stability.
• Parameter Assignment: Assigns atomic charge and radius parameters using selectable force fields.
• pK(a) Estimation and Protonation: Estimates pK(a) values and protonates residues using frameworks such as PROPKA with consideration of hydrogen-bonding.
• Ligand Parameterization: Incorporates ligand parameterization using methods such as PEOE_PB charge.
• Expanded Force Field Support: Supports an expanded set of force fields and user-defined parameters via XML input files.

Scientific Applications:

• Continuum Electrostatics Calculations: Prepares structures for Poisson-Boltzmann and Generalized Born electrostatics calculations.
• Molecular Energetics and Dynamics: Enables analysis of electrostatic contributions to biomolecular structure, energetics, and dynamics.
• Ligand Binding and Interaction Modeling: Facilitates parameterization of ligands for studies of binding and intermolecular interactions.
• Large-scale Structural Studies: Supports preparation of macromolecular structures for systems- and genome-wide biophysical analyses.

Methodology:

Converts PDB files to PQR by adding missing atoms, optimizing hydrogen bonds, assigning atomic charges and radii via force fields (with XML parameter support), estimating titration states with PROPKA, and performing ligand parameterization such as PEOE_PB charge assignment.