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A Self-Organizing Map of Amino Acids with Their Local Environments in Proteins by Using Pairwise-Contact Energy Parameters

Title
A Self-Organizing Map of Amino Acids with Their Local Environments in Proteins by Using Pairwise-Contact Energy Parameters
Authors
Cheon, Moo KyungHeo, Mu YoungChang, Ik Soo김충락
DGIST Authors
Chang, Ik Soo
Issue Date
2005-11
Citation
Journal of the Korean Physical Society, 47(3), 895-899
Type
Article
Article Type
Article
Keywords
Self-organizing mapProtein score functionClassication of amino acids
ISSN
0374-4884
Abstract
Based on the 180 X 180 pairwise-contact energy parameters between 20 amino acids incorporating their 9 local environments in proteins, the classification of 180 types of amino acids is presented by the self-organizing map. We demonstrate that the physico-chemical features of the amino acids are well captured in the 180 x 180 pairwise-contact energy parameters and that they agree with their known biological characters in the simultaneous aspects of secondary structures, hydrophobicity, and the existence probability of amino acids under various environments in protein structures. Our result justifies the use of these energy parameters for the recognition of protein folds.
URI
http://hdl.handle.net/20.500.11750/5838
Publisher
한국물리학회
Related Researcher
  • Author Chang, Ik Soo Theoretical and Computational Biophysics Laboratory
  • Research Interests Theoretical and Computational Biophysics; Supercomputing Simulation of Biomolecules; 이론?계산 생물물리학; 통계물리학; 단백질체의 슈퍼컴퓨터 모델링 및 시물레이션
Files:
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Collection:
Department of Brain and Cognitive SciencesTheoretical and Computational Biophysics Laboratory1. Journal Articles


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