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Probik: Protein Backbone Motion by Inverse Kinematics

University of North Carolina, Chapel Hill, NC 27599, USA

David O'Brien

University of North Carolina, Chapel Hill, NC 27599, USA

Jack Snoeyink

University of North Carolina, Chapel Hill, NC 27599, USA, snoeyink{at}cs.unc.edu

To investigate the parameters of the protein design problem that we are exploring in collaboration with biochemists, we have 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 parametrize the space of backbone motions.

Key Words: protein design • backbone geometry • six revolute joint manipulator • Denavit-Hartenberg frames

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