Structural Biology Software Database
Structural Biology Software Database

Application Index Record

Category: Molecular Dynamics
SDA: Simulation of Diffusional Association of proteins
Last Update: 03-23-2007

SDA permits Brownian dynamics simulations to be carried out and the rates of bimolecular diffusional association of 2 molecules, e.g. 2 proteins, to be computed given the atomic structure of the bound complex of the 2 molecules. Proteins are represented as rigid bodies with all-atom detail accuracy. The interaction between the molecules is given by an approximation to the Poisson-Boltzmann equation-derived electrostatic interaction. Association events are monitored by means of different criteria.


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