Binder Design

OVERVIEW

Binder Design is a tool for designing binders using RFDiffusion. RFDiffusion is a method for structure generation (with or without conditional information) useful for protein design challenges. RFDiffusion is capable of motif scaffolding, unconditional protein generation, symmetric motif scaffolding, binder design, and more. RFDiffusion GitHub repository

RUNNING Binder Design

To begin, open an existing project or create one in Bench. Click on a structure collection on the left in the ‘Structures’ panel, or load one using the ‘Structure Loader’ button. Once you have selected the desired structure to run Binder Design on click the ‘Binder Design’ button in the ‘Actions’ panel to open a Binder Design tab. Use the selector dropdowns and other inputs, or toggle ‘Advanced Mode’ to enter RFDiffusion parameters directly. If using Advanced Mode the following format should be used, with any additional custom arguments specified on new lines below:

contigmap.contigs=[A1-100/0 50-50]
inference.num_designs=1000
ppi.hotspot_res=[A1,A2,A7,A41,A58,A60,A61,A62,A63]

When you have configured your desired inputs click ‘Save & Run’. Once the job completes you will see an output collection created with the results.