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ProtoFold: Part I — Nanokinematics for Analysis of Protein Molecules

[+] Author Affiliations
Kazem Kazerounian, Khalid Latif, Kimberly Rodriguez

University of Connecticut, Storrs, CT

Carlos Alvarado

Polytechnic University of Puerto Rico, Hato Rey, Puerto Rico

Paper No. DETC2004-57243, pp. 645-658; 14 pages
doi:10.1115/DETC2004-57243
From:
  • ASME 2004 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference
  • Volume 2: 28th Biennial Mechanisms and Robotics Conference, Parts A and B
  • Salt Lake City, Utah, USA, September 28–October 2, 2004
  • Conference Sponsors: Design Engineering Division and Computers and Information in Engineering Division
  • ISBN: 0-7918-4695-4 | eISBN: 0-7918-3742-4
  • Copyright © 2004 by ASME

abstract

Proteins are evolution’s mechanisms of choice. Study of nano-mechanical systems must encompass an understanding of the geometry and conformation of protein molecules. Proteins are open or closed loop kinematic chains of miniature rigid bodies connected by revolute joints. The Kinematics community is in a unique position to extend the boundaries of knowledge in nano biomechanical systems. ProtoFold is a software package that implements novel and comprehensive methodologies for ab initio prediction of the final three-dimensional conformation of a protein, given only its linear structure. In this paper, we present the methods utilized in the kinematics notion and kinematics analysis of protein molecules. The kinematics portion of ProtoFold incorporates the Zero-Position Analysis Method and draws upon other recent advances in robot manipulation theories. We claim that the methodology presented is a computationally superior and more stable alternative to traditional molecular dynamics simulation techniques.

Copyright © 2004 by ASME
Topics: Proteins

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