By Rebecca Wade
Software for simulating macromolecular diffusion
SDA (Simulation of Diffusional Association) is a Brownian dynamics simulation code that can be used to simulate the diffusion of biomacromolecules in aqueous solution. It is particularly useful for studying the effects of electrostatic steering on molecular diffusional association processes. The association of two molecules can be simulated to compute bimolecular diffusional association rate constants under dilute conditions and to predict the structures of diffusional encounter complexes, subject to biochemical constraints. SDA can also be used to simulate concentrated protein solutions and to investigate the diffusional association of proteins with solid surfaces. SDA 7 is available for standalone use and some of the functionality is implemented in the webSDA webserver.
Bruce et al, (2015) Liquids-Lecture Notes, IAS Series, 28, 259