Open AccessClassifying Protein Specific Residue Structures Based on Graph Mining
Author(s) -
Sun-Yuan Hsieh,
Chia-Wei Lee,
Zong-Ying Yang,
Heng-Wei Wang,
Jun-Han Yu,
Bo-Cheng Chan,
Tai-Ling Ye
Publication year - 2018
Publication title -
ieee access
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.587
H-Index - 127
ISSN - 2169-3536
DOI - 10.1109/access.2018.2872496
Subject(s) - aerospace , bioengineering , communication, networking and broadcast technologies , components, circuits, devices and systems , computing and processing , engineered materials, dielectrics and plasmas , engineering profession , fields, waves and electromagnetics , general topics for engineers , geoscience , nuclear engineering , photonics and electrooptics , power, energy and industry applications , robotics and control systems , signal processing and analysis , transportation
We proposed a 3-D protein structure using a simple and connected graph, where nodes indicate amino acids and edges represent contact distances between amino acids. Based on these graph structures, we present a graph mining algorithm to determine the crucial subgraphs in these graphs, which can be applied to classify protein structural families. The proposed algorithm was compared with BLAST, BLAT, and DALI. Moreover, an experiment was conducted, in which characteristic sub-structural patterns were found in several protein families within the Protein Data Bank.
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