SDA 7.2.3 / webSDA 1.0 – Simulation of Diffusional Association

SDA 7.2.3 / webSDA 1.0


SDA simulates the diffusional association of two proteins/molecules or a protein/molecule to a solid state surface. If the atomic structure of the bound complex is known, SDA can be used to calculate bimolecular association rates. It can also be used to record Brownian dynamics trajectories or encounter complexes and calculate bimolecular electron transfer rate constants. SDA may also be used for rigid-body docking to predict the structure of protein-protein encounter complexes or the orientation in which a protein binds to a surface.

webSDA is a web server to simulate macromolecular diffusional association.


Molecular and Cellular Modeling ,HITS gGmbH




  • Linux





webSDA: a web server to simulate macromolecular diffusional association.
Yu X, Martinez M, Gable AL, Fuller JC, Bruce NJ, Richter S, Wade RC.
Nucleic Acids Res. 2015 Jul 1;43(W1):W220-4. doi: 10.1093/nar/gkv335.

Gabdoulline RR and Wade RC.
Simulation of the Diffusional Association of Barnase and Barstar.
Biophys. J. (1997) 72, 1917-1929.