MacroDox Brownian Dynamics Software. MacroDox is software for setting up and running Brownian dynamics simulations capable of calculating the rate of attainment of optimum docking conformations of protein-protein, protein-DNA, and other complexes. In its simplest application the software allows the user to compute and display physical properties of individual proteins and nucleic acids starting from coordinate information downloaded from the Protein Data Bank. Such properties would include surrounding electrostatic fields, dipole moment, radius of gyration, titration curves, protonation status of titratible sites, and solvent accessible surfaces. In its most advanced application the software would utilize this information to generate a representative search of plausible docked complexes using a Brownian dynamics algorithm and make predictions of the most energetically stable complexes. Exploiting the sophistication of our existing Brownian Dynamics methodology, the program would allow an automated force-guided search of docked conformers which would avoid trapping in local energy minima. Future implementations will further allow the user to intervene and manipulate the conformers as well. The software complements other types of programs which are less able to accurately handle electrostatic interactions. Additionally the program is able to compute the bimolecular diffusive rate constant of attainment of docked complexes by Brownian dynamics.

Keywords for this software

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