MacroDox Overview

• Imports Protein Data Bank(PDB)-formatted protein coordinate files or HyperChem-formatted files.
• Assigns masses and charges to every atom from a standard set of charges.
• Performs a Tanford-Kirkwood calculation to estimate the pKa's and mean charge on titratible amino acids.
• Assigns partial charges on residues based on Tanford-Kirkwood model.
• Computes various properties of the protein, such as solvent exposure of every atom, dipole moments, atom number density in concentric shells, estimated spherical radius, radius of gyration, translational diff coef, rotational diff coeff, and a list of atoms near the dipole vector ends.
• Computes electrostatic field grids around the protein based on iterative solutions of the linear and full Poisson-Boltzmann equation.
• Provides menus to set up and run Brownian Dynamics docking simulations on proteins. Either a full-blown atomic scale rough topology can be treated or the reaction between two spheres with embedded charges.
• A certain amount of analysis of complexes generated through Brownian Dynamics.

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