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Webserver for Simulation of Diffusional Association (SDA): making life much easier to simulate macromolecular diffusion.

Step 0: Upload your solutes for the simulation

Please upload the macromolecules (solutes) you want to simulate. The simplest option is to type in a PDB ID, and select the chains that you want. The pH must be specified so that PDB2PQR can protonate titratable residues. More advanced users may want to try uploading a PDB file that they have created themselves. For very specific use cases, you can upload a PQR file. PQR files can be created using PDB2PQR. More details can be found in the FAQ

Solute name

Input type

Solute information

PDB ID

pH

Add conformation

Barnase

PDB file	PQR file	Id	pH	Net charge	Ionic strength	Non-hydrogen PDB	Electrostatic grid	Effective charges	Eletrostatic desolvation grid	Apolar desolvation grid	Lennard-Jones repulsive grid
	Barnase.pqr	5718	7.0

Barstar

PDB file	PQR file	Id	pH	Net charge	Ionic strength	Non-hydrogen PDB	Electrostatic grid	Effective charges	Eletrostatic desolvation grid	Apolar desolvation grid	Lennard-Jones repulsive grid
	Barstar.pqr	5719	7.0

Lysozyme_pH6

PDB file	PQR file	Id	pH	Net charge	Ionic strength	Non-hydrogen PDB	Electrostatic grid	Effective charges	Eletrostatic desolvation grid	Apolar desolvation grid	Lennard-Jones repulsive grid
	Lysozyme_pH6.pqr	5720	7.0

Which SDA method would you like to use?

More info»

In the SDA docking method, SDA is used to generate structures of the diffusional encounter complex for two input solutes. SDA employs Brownian dynamics to perform the sampling of the positions of the solutes, accounting for electrostatic and non-polar intermolecular forces. The solutes are treated as rigid bodies. Flexibility can be accounted for by providing several different conformations for one of the solutes.

SDA docking

More info»

In the SDA association method, the bimolecular diffusional association rate constant for two input solutes is computed. The relative diffusional motion of the two solutes is simulated by Brownian dynamics subject to interaction forces. Because of their long range, electrostatic interactions can have a major impact of the rates of association between two solutes. The effects of electrostatic steering and the influence of changes in pH, ionic strength or protein mutation on association rates can be investigated. The solutes are treated as rigid bodies. Flexibility can be accounted for by providing several different conformations for one of the solutes.

SDA association

More info»

In the SDA multiple molecules method, the diffusive motion of several hundred macromolecules can be simulated by Brownian dynamics subject to electrostatic, non-polar and steric intermolecular forces. Simulation with several types of molecule, and different conformations of each type of molecule, can be performed.

SDA multiple molecules