This example uses the crystal structure of the UBA domain from Cbl-b ubiquitin ligase in complex with ubiquitin (PDB 2OOB) to demonstrate the LZerD web server. Below, ubiquitin and the UBA domain have both been loaded as receptor and ligand respectively.
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 residue 44 of chain B of the receptor structure should be part of the protein-protein interface. A receptor constraint has been filled in below with this residue. This constraint means that only models where that residue is within 10 Å of the UBA domain will appear in the output.