PDB_Hydro

PDB_Hydro computes electrostatic properties and models solvation of biological macromolecules, including proteins and DNA, using a Generalized Poisson-Boltzmann-Langevin equation that avoids assuming a constant dielectric in the solvent region.

Key Features:

• Electrostatic modeling (GPBLE): Computes electrostatic properties using the Generalized Poisson-Boltzmann-Langevin equation to model macromolecule–solvent electrostatics without a constant solvent dielectric.
• Sequence mutation: Introduces mutations into macromolecular sequences for subsequent structural and electrostatic analysis.
• Structural reconstruction: Reconstructs missing side-chain and main-chain atoms in macromolecular structures.
• Solvent modeling and water profiles: Generates solvent density and detailed water profiles to characterize the aqueous environment around macromolecules.

Scientific Applications:

• Low-resolution X-ray diffraction fitting: Incorporates solvent density information to improve fits at low resolution in X-ray diffraction analyses.
• Docking and interaction energy calculation: Provides detailed water profiles that can enhance calculation of interaction energies between ligands and receptors during docking simulations.

Methodology:

Computational methods explicitly include solving the Generalized Poisson-Boltzmann-Langevin equation for electrostatics, sequence mutation routines, reconstruction of missing side‑chain and main‑chain atoms, and generation of solvent/water density profiles.