Protein structure search and local structure characterization |
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| Authors: | Shih-Yen Ku Yuh-Jyh Hu |
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| Affiliation: | (1) Department of Computer Science, National Chiao Tung University, 1001 University Rd., Hsinchu, Taiwan;(2) Institute of Statistics, Academia Sinica, Taipei, Taiwan;(3) Institute of Biomedical Engineering, National Chiao Tung University, 1001 University Rd., Hsinchu, Taiwan |
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| Abstract: | Background Structural similarities among proteins can provide valuable insight into their functional mechanisms and relationships. As the number of available three-dimensional (3D) protein structures increases, a greater variety of studies can be conducted with increasing efficiency, among which is the design of protein structural alphabets. Structural alphabets allow us to characterize local structures of proteins and describe the global folding structure of a protein using a one-dimensional (1D) sequence. Thus, 1D sequences can be used to identify structural similarities among proteins using standard sequence alignment tools such as BLAST or FASTA. |
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