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An Optimized Kinematic Mobility Analysis of Protein Molecules

[+] Author Affiliations
Ahmet Demirtas, Zahra Shahbazi

Manhattan College, Riverdale, NY

Paper No. DETC2014-34783, pp. V05AT08A014; 8 pages
doi:10.1115/DETC2014-34783
From:
  • ASME 2014 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference
  • Volume 5A: 38th Mechanisms and Robotics Conference
  • Buffalo, New York, USA, August 17–20, 2014
  • Conference Sponsors: Design Engineering Division, Computers and Information in Engineering Division
  • ISBN: 978-0-7918-4636-0
  • Copyright © 2014 by ASME

abstract

Understanding the 3D structure and consequently the motion of protein molecules contributes to simulate their function. Modeling protein molecules as kinematic chains has been used to predict protein molecules flexible and rigid regions as well as their degrees of freedom to predict their mobility. However, high computational cost for relatively large molecules is one of the major challenges in this field.

In this paper we have combined our previously developed rigidity analysis (ProtoFold) with pebble game thus improving computational cost of our simulation. Here, we have determined the required time for all steps of ProtoFold and subsequently the most time consuming step. Results have shown that finding rigid loops inside the protein structure using graph theory and Grübler-Kutzbach criterion is the slowest part of the procedure, taking an average of 75% of the time required for the rigidity analysis. Therefore we have replaced this step with pebble game. The modified method has been applied to a random group of protein molecules and its efficiency in significantly improving the simulation speed has been verified.

Copyright © 2014 by ASME

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