Probik: Protein Backbone Motion by Inverse Kinematics

Abstract

To investigate the parameters of the protein design problem that we are exploring in collaboration with biochemists, we developed a tool that uses inverse kinematics to support moving small fragments of protein backbone, while respecting biochemists’ desires to “remain in favorable regions of the Ramachandran plot” and “preserve ideal geometry.” By presenting estimates of derivatives in response to motion, we are able to refine these qualitative desires as we work with our collaborators. We then explore low dimensional bases to parameterize the space of backbone motions.