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A Self-Organizing Map of Amino Acids with Their Local Environments in Proteins by Using Pairwise-Contact Energy Parameters
- A Self-Organizing Map of Amino Acids with Their Local Environments in Proteins by Using Pairwise-Contact Energy Parameters
- Cheon, Moo Kyung; Heo, Mu Young; Chang, Ik Soo; Kim, C
- DGIST Authors
- Chang, Ik Soo
- Issue Date
- Journal of the Korean Physical Society, 47(3), 895-899
- Article Type
- Self-organizing map; Protein score function; Classication of amino acids
- 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.
- Korean Physical Society
- Related Researcher
Theoretical and Computational Biophysics Laboratory
Theoretical and Computational Biophysics; Supercomputing Simulation of Biomolecules; 이론?계산 생물물리학; 통계물리학; 단백질체의 슈퍼컴퓨터 모델링 및 시물레이션
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- Department of Brain and Cognitive SciencesTheoretical and Computational Biophysics Laboratory1. Journal Articles
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