SDA (Simulation of Diffusional Association) is a software package that can be used to carry out Brownian dynamics simulations of the diffusional association of solute molecules, e.g. proteins in a continuum aqueous solvent. The interaction between the molecules is given by an approximation to the Poisson-Boltzmann equation-derived electrostatic interaction. If the 3D structure of the bound complex is known, SDA can be used to calculate bimolecular association rates using a user-defined set of intermolecular contact distances as reaction criteria. It can also be used to perform rigid-body docking to record Brownian dynamics trajectories or encounter complexes and to calculate bimolecular electron transfer rate constants. SDA can also be used to simulate the diffusion of multiple proteins, in dilute or concentrated solutions, e.g., to study the effects of macromolecular crowding.

 

webSDA: SDA can also be launched using a webserver. (http://mcm.h-its.org/webSDA)

Application/Keywords: Brownian Dynamics Simulations, Bimolecular association rate constants calculation, Rigid-body Docking, Macromolecular Crowding