This example uses the crystal structure of cytochrome c oxidase (PDB 1M56) to demonstrate the Mem-LZerD web server. Below, subunit 1 and subunit 3 have been loaded as receptor and ligand respectively. Note that both subunits in the example have already been oriented in the membrane as part of their inclusion in the OPM database.
The clustering cutoff has been left at its default value of 4 Å. Increasing this value would cause more models to be discarded during clustering, thus reducing the running time of the model set scoring.
The surface reduction cutoff has been set to its coarsest setting of 1e-2. Compared to using the default value of 1e-4, this will cause the docking search to be less exhaustive, thus reducing the running time.
Specifying a job title and comments can help you keep track of your LZerD jobs.
In this example, we know that unconstrained docking is sufficient to model the interface, and the constraints section is thus left blank.