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Analyzing Motion Properties of Proteins Affected by Localized Structures From a Robot Kinematics Perspective

[+] Author Affiliations
Keisuke Arikawa

Kanagawa Institute of Technology, Atsugi, Kanagawa, Japan

Paper No. DETC2015-47010, pp. V05AT08A039; 10 pages
  • ASME 2015 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference
  • Volume 5A: 39th Mechanisms and Robotics Conference
  • Boston, Massachusetts, USA, August 2–5, 2015
  • Conference Sponsors: Design Engineering Division, Computers and Information in Engineering Division
  • ISBN: 978-0-7918-5712-0
  • Copyright © 2015 by ASME


On the basis of robot kinematics, we have thus far developed a method for predicting the motion of proteins from their 3D structural data given in the Protein Data Bank (PDB data). In this method, proteins are modeled as serial manipulators constrained by springs and the structural compliance properties of the models are evaluated. We focus on localized instead of whole structures of proteins. Employing the same model used in our method of motion prediction, the motion properties of the localized structures and the relation between the motion properties of localized and whole structures are analyzed. First, we present a method for graphically expressing the deformation of objects with a complex shape, such as proteins, by approximating the shape as a rectangular prism with a mesh on its surface. We then formulate a method for comparing the motion properties of localized structures cleaved from the whole structure and those remaining in it by expressing the motion of the latter using the decomposed motion modes of the former according to the structural compliance. Finally, we show a method for evaluating the effect of a localized structure on the motion properties of proteins by applying forces to localized structures. In the formulations, we demonstrate applications as illustrative examples using the PDB data of a real protein.

Copyright © 2015 by ASME



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