Protein Structure Comparison and Visualization Tools on Cloud Platform

  • Yaw-Ling Lin
  • Chen-En Hsieh
  • Guan-Jie Hua
  • Che-Lun Hung
Part of the Smart Innovation, Systems and Technologies book series (SIST, volume 20)

Abstract

The biological function of a protein molecule is decided by its 3D-shape, which eventually determines how the molecule interacts with other molecules in living cells. Identifying similar structures between proteins provide the opportunity to recognize homology that is undetectable by sequence comparison. Thus comparison and alignment of protein structures represents a powerful means of discovering functions, yielding direct insight into the molecular mechanisms.

This paper proposes approaches in providing visualization tools for pairwise 3D protein structure alignment; our web service takes advantage of the Map Reduce paradigm as means of management and parallelizing tools under massive number of protein pairs examined under the experiment. It shows that our previously proposed sequential combinatorial algorithms are well parallelized under the map/reduce platform. These methods are tested on the real-world data obtained in from the RCSB PDB data set; the computation efficiency can be effectively improved proportional to the number of processors being used.

Keywords

protein structures comparisons bioinformatics visualization VRML MapReduce Hadoop cloud computing 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • Yaw-Ling Lin
    • 1
  • Chen-En Hsieh
    • 1
  • Guan-Jie Hua
    • 1
  • Che-Lun Hung
    • 2
  1. 1.Department of Computer Science and Information EngineeringProvidence UniversityTaichungTaiwan
  2. 2.Department of Computer Science and Communication EngineeringProvidence UniversityTaichungTaiwan

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