我們提供了一個根據對PDB資料庫中69534筆蛋白質資料做特徵分析而得的方法，這個方法可以應用在蛋白質二級結構預測工具像是PSIPRED的修正。另外，我們採用了bi-gram和classification的技巧去提昇這個方法修正的準確率。這個方法分析了二十種蛋白質氨基酸與蛋白質二級結構之間的關係，並運用分析出來的結果修正了PSIPRED所預測出來的二級結構。結果顯示了我們的方法對於All-Beta分類的蛋白質特別有效。

We purpose a method to refine the protein secondary structure prediction tools such as PSIPRED according the pattern analysis of 69534 protein data stored in PDB database. Besides, we use a bi-gram approach and classification to increase the accuracy of refinement. The method we purposed analyses the relation between twenty kinds of amino acid and protein secondary structures, and use the stasis results to refine the predicted secondary structures which are hard cases for PSIPRED. The experiment result reveals that our method is effective for all-beta entries.

1. McGuffin,L.J. and Jones,D.T. (2003) Benchmarking secondary structure prediction for fold recognition. Proteins, 52, 166-175.
2. Bonneau,R., Tsia,J., Ruczinski,I., Chivian,D., Rohl, Strauss,C.E.M. and Baker, D. (2001) Rosetta in CASP4: Progress in ab initio protein structure prediction. Proteins, 45, 119-126.
3. Phillips, A., Janies, D. and Wheeler, W. (2000) Multiple Sequence Alignment in Phylogenetic Analysis. Molecular Phylogenetics and Evolution, 16, 317-330.
4. Vapnik,V.N. (1995) The Nature of Statistical Learning Theory, Springer-Verlag.
5. Rost,B. (1993) Prediction of Protein Secondary Structure at Better than 70% accuracy. J. Mol. Biol., 232, 584-599.
6. Jones,D.T. (1999) Protein Secondary Structure Prediction Based on Position-specific Scoring Matrices. J. Mol. Biol., 292, 195-202.
7. Altschul,S.F., Madden,T.L., Schaffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. 1997 Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
8. W. Kabsch and C. Sander. A dictionary of protein secondary structure. Biopolymers, 22:2577-2637, 1983.
9. Rost,B. (2001) Review: protein secondary structure prediction continues to rise. J. Struct. Biol., 134, 204-218.
10. Berman, H.M., Westbrook,J., Feng,Z., Gilliland,G.., Bhat,T.N., Weissig,H., Shindyalov,I.N. and Bourne,P.E. (2000) The Protein Data Bank. Nucleic Acids Res., 28, 235-242.
11. Michael Collins. A new statistical parser based on bigram lexical dependencies. In Proceedings of the 34th Annual Meeting of the Association of Computational Linguistics, Santa Cruz, CA. 1996. pp.184-191.
12. Murzin AG, Brenner SE, Hubbard T, Chothia C (1995). "SCOP: a structural classification of proteins database for the investigation of sequences and structures". J. Mol. Biol. 247 (4): 536-40.
13. Orengo, C.A., Michie, A.D., Jones, S., Jones, D.T., Swindells, M.B., and Thornton, J.M. (1997) CATH- A Hierarchic Classification of Protein Domain Structures. Structure. Vol 5. No 8. p.1093-1108.
14. Ying-Chuan Liu. (2007). Protein Secondary Structure Prediction Based on Linear Transformation and Normalization Methods. The Master of Science Degree Program, NTHU.