ProteinMPNN

OVERVIEW

ProteinMPNN is a tool that takes as input a PDB file and rapidly generates new sequences predicted to fold to the backbone of the input PDB. ProteinMPNN GitHub repository

RUNNING ProteinMPNN

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 proteinMPNN on click the ‘proteinMPNN’ button in the ‘Actions’ panel to open a proteinMPNN tab. When you have configured your desired sampling temperature and number of designs click ‘Save & Run’. Once the job completes you will see an output sequence collection created. Sequences within this collection can be selected and used to run AI Folding jobs.