Citation: DAI Zhi-Jun, ZHOU Wei, YUAN Zhe-Ming. A Novel Method of Nonlinear Rapid Feature Selection for High Dimensional Data and Its Application in Peptide QSAR Modeling Based on Support Vector Machine[J]. Acta Physico-Chimica Sinica, ;2011, 27(07): 1654-1660. doi: 10.3866/PKU.WHXB20110735 shu

A Novel Method of Nonlinear Rapid Feature Selection for High Dimensional Data and Its Application in Peptide QSAR Modeling Based on Support Vector Machine

DAI Zhi-Jun ^1,2 ,
ZHOU Wei ¹ ,
YUAN Zhe-Ming ^1,2,

1.
1. College of Bio-safety Science and Technology, Hunan Agricultural University, Changsha 410128, P. R. China;
2. Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization, Changsha 410128, P. R. China

Received Date: 24 March 2011
Available Online: 3 June 2011
Fund Project: 湖南省杰出青年科学基金(10JJ1005) (10JJ1005) 高等学校博士点基金(200805370002) (200805370002)

Each amino acid residue of one peptide was characterized directly by 531 physicochemical property parameters. Based on support vector regression (SVR) we developed a new nonlinear rapid feature selection method for high dimensional data, which was applied to a quantitative sequence- activity relationship (QSAR) study of two peptide systems (bitter tasting thresholds and angiotensin converting enzyme inhibitors). In both systems, 10 descriptors with clear meaning were reserved. We established a SVR model for both peptide systems using the reserved descriptors of the peptides. For both models the accuracies of fitting, the leave-one-out cross validation, and the external prediction improved significantly compared with the results reported in literature. To enhance the interpretability of the models, significance tests of the nonlinear regression model, single-factor relative importance, and a single-factor effect analysis were carried out. The new method has broad application prospects for regression forecasting of high dimensional data such as QSAR modeling of peptide or proteins.
- High dimensional feature,
- Feature selection,
- Peptide,
- Quantitative sequence-activity relationship,
- Support vector machine
1. [1]
  
  (1) Ding, J. L.; Ho, B. Drug Dev. Res. 2004, 62 (4), 317.
2. [2]
  (2) Sneath, P. H. A. J. Theor. Biol. 1966, 12 (2), 157.
3. [3]
  (3) Kidera, A.; Konishi, Y.; Oka, M.; Ooi, T.; Scheraga, H. A. J. Protein Chem. 1985, 4 (1), 23.
4. [4]
  (4) Hellberg, S.; Eriksson, L.; Jonsson, J.; Lindgren, F.; Sjöström, M.; Skagerberg, B.;Wold, S.; Andrews, P. Int. J. Pept. Protein Res. 1991, 37 (5), 414.
5. [5]
  (5) Sandberg, M.; Eriksson, L.; Jonsson, J.; Sjöström, M.;Wold, S. J. Med. Chem. 1998, 41 (14), 2481.
6. [6]
  (6) Liang, G. Z.; Mei, H.; Zhou, P.; Zhou, Y.; Li, Z. L. Acta Phys. -Chim. Sin. 2006, 22 (3), 388. [梁桂兆, 梅虎, 周鹏, 周原, 李志良. 物理化学学报, 2006, 22 (3), 388.]
7. [7]
  (7) Zhou, Y.; Mei, H.; Yang, L.; Zhou, P.; Yang, S. B.; Li, Z, L. Chem. J. Chin. Univ. 2007, 28 (7), 1263. [周原, 梅虎, 杨力, 周鹏, 杨善斌, 李志良. 高等学校化学学报, 2007, 28 (7), 1263.]
8. [8]
  (8) Yang, S. B.; Xia, Z. N.; Shu, M.; Mei, H.; Lü, F. L.; Zhang, M.; Wu, Y. Q.; Li, Z. L. Chem. J. Chin. Univ. 2008, 29 (11), 2213. [杨善彬, 夏之宁, 舒茂, 梅虎, 吕凤林, 张梅, 吴玉乾, 李志良. 高等学校化学学报, 2008, 29 (11), 2213.]
9. [9]
  (9) Liang, G. Z.; Zhou, P.; Zhou, Y.; Zhang, Q. X.; Li, Z. L. Acta Chim. Sin. 2006, 64 (5), 393. [梁桂兆, 周鹏, 周原, 张巧霞, 李志良. 化学学报, 2006, 64 (5), 393.]
10. [10]
  (10) Li, Z. L.; Li, G. R.; Shu, M.; Sun, J. Y.; Yang, S. B.; Mei, H.; Zhang, M. J.; Zhou, P.;Wu, S. R.; Chen, G. H.; Lü, F. L.; Lü, T. T. Sci. China Ser. B: Chem. 2008, 38 (8), 745. [李志良, 李根容, 舒茂, 孙家英, 杨善斌, 梅虎, 张梦军, 周萍, 吴世荣, 陈国华, 吕凤林, 吕廷亭. 中国科学B辑: 化学, 2008, 38 (8), 745.]
11. [11]
  (11) Kawashima, S.; Pokarowski, P.; Pokarowska, M.; Kolinski, A.; Katayama, T.; Kanehisa, M. Nucleic Acids Res. 2008, 36, D202.
12. [12]
  (12) Dash, M.; Liu, H. Intell. Data Anal. 1997, 1 (3), 131.
13. [13]
  (13) Kohavi, R.; John, G. H. Artif. Intel. 1997, 97 (1-2), 273.
14. [14]
  (14) Cover, T. M. IEEE Trans. Syst. Man Cybern. 1974, 4 (2), 116.
15. [15]
  (15) Colannino, J.; Juban, J. The Best K Measurements are Not the K Best. http://cgm.cs.mcgill.ca/-athens/cs644/Projects/2004/ JustinColannino-JeremieJuban/best.html, (accessed Mar 22, 2011).
16. [16]
  (16) Cortes, C.; Vapnik, V. Mach. Learn. 1995, 20 (3), 273.
17. [17]
  (17) Hou, T. J.; Xu, Z.; Zhang,W.; McLaughlin, A,W.; Case, D. A.; Xu, Y.;Wang,W. Mol. Cell. Proteomics 2009, 8, 639.
18. [18]
  (18) Hou, T. J.; Zhang,W.; Case, D. A.;Wang,W. J. Mol. Biol. 2008, 376, 1201.
19. [19]
  (19) Wang, H.; Zhang, B. J.; Liu, X. Z.; Luo, D. Z.; Zhong, S. B. Adv. Mater. Res. 2011, 143, 1254.
20. [20]
  (20) Zhang, Y. M.; Jin, Q.;Wang, S. T.; Ren, R. Comput. Biol. Med. 2011, 41 (5), 271.
21. [21]
  (21) Yuan, Z. M.; Zhang, Y. S.; Xiong, J. Y. Scientia Agricultura Sinica 2008, 41 (8), 2485. [袁哲明, 张永生, 熊洁仪. 中国农业科学, 2008, 41 (8), 2485.]
22. [22]
  (22) Zhang, Y. S.; Yuan, Z. M.; Xiong, J. Y.; Zhou, T. J. Acta Ecologica Sinica 2007, 27 (6), 2419. [张永生, 袁哲明, 熊洁仪, 周铁军. 生态学报, 2007, 27 (6), 2419.]
23. [23]
  (23) Tan, X. S.;Wang, Z. M.; Tan, S. Q.; Yuan, Z. M.; Xiong, X. Y.; Journal of System Simulation 2009, 21 (24), 7795. [谭显胜, 王志明, 谭泗桥, 袁哲明, 熊兴耀. 系统仿真学报, 2009, 21(24), 7795.]
24. [24]
  (24) Yuan, Z. M.; Tan, X. S. Acta Agronomica Sinica 2010, 36 (7), 1176. [袁哲明, 谭显胜. 作物学报, 2010, 36 (7), 1176.]
25. [25]
  (25) Tan, X. S.; Yuan, Z. M.; Zhou, T. J.;Wang, C. J.; Xiong, J. Y. Chem. J. Chin. Univ. 2008, 29 (1), 95. [谭显胜, 袁哲明, 周铁军, 王春娟, 熊洁仪. 高等学校化学学报, 2008, 29 (1), 95.]
26. [26]
  (26) Tropsha, A.; Gramatica, P.; mbar, V. K. QSAR Comb. Sci. 2003, 22 (1), 69.
27. [27]
  (27) Cocchi, M.; Johansson, E. Quant. Struct. -Act. Relat. 1993, 12(1), 1.
28. [28]
  (28) Collantes, E. R.; Dunn,W. J. J. Med. Chem. 1995, 38 (14), 2705.
29. [29]
  (29) Mei, H.; Zhou, Y.; Sun, L. L.; Li, Z. L. Chemistry 2005, (7), 534. [梅虎, 周原, 孙立力, 李志良. 化学通报, 2005, (7), 534.]
30. [30]
  (30) Mei, H.; Liang, G. Z.; Zhou, Y.; Li, Z. L. Chin. Sci. Bull. 2005, 50 (16), 1703. [梅虎, 梁桂兆, 周原, 李志良. 科学通报, 2005, 50 (16), 1703.]
31. [31]
  (31) Richardson, J. S.; Richardson, D. C. Science 1988, 240 (4859), 1648.
32. [32]
  (32) Cornette, J. L.; Cease, K. B.; Margalit, H.; Spouge, J. L.; Berzofsky, J. A.; DeLisi, C. J. Mol. Biol. 1987, 195 (3), 659.
33. [33]
  (33) Pliška, V.; Schmidt, M.; Fauchère, J. L. J. Chromatogr. A 1981, 216, 79.
34. [34]
  (34) Hassell, C. H.; Krohn, A.; Moody, C. J.; Thomas,W. A. J. Chem. Soc. Perkin. Trans. 1 1984, 23, 155.
1. [1]
  Yixuan Zhu , Qingtong Wang , Jin Li , Lin Chen , Junlong Zhao . Blog of Oxytocin. University Chemistry, 2024, 39(9): 134-140. doi: 10.12461/PKU.DXHX202310090
2. [2]
  Shihui Shi , Haoyu Li , Shaojie Han , Yifan Yao , Siqi Liu . Regioselectively Synthesis of Halogenated Arenes via Self-Assembly and Synergistic Catalysis Strategy. University Chemistry, 2024, 39(5): 336-344. doi: 10.3866/PKU.DXHX202312002
3. [3]
  Peiran ZHAO , Yuqian LIU , Cheng HE , Chunying DUAN . A functionalized Eu³⁺ metal-organic framework for selective fluorescent detection of pyrene. Chinese Journal of Inorganic Chemistry, 2024, 40(4): 713-724. doi: 10.11862/CJIC.20230355
4. [4]
  Jing SU , Bingrong LI , Yiyan BAI , Wenjuan JI , Haiying YANG , Zhefeng Fan . Highly sensitive electrochemical dopamine sensor based on a highly stable In-based metal-organic framework with amino-enriched pores. Chinese Journal of Inorganic Chemistry, 2024, 40(7): 1337-1346. doi: 10.11862/CJIC.20230414
5. [5]
  Yuanpei ZHANG , Jiahong WANG , Jinming HUANG , Zhi HU . Preparation of magnetic mesoporous carbon loaded nano zero-valent iron for removal of Cr(Ⅲ) organic complexes from high-salt wastewater. Chinese Journal of Inorganic Chemistry, 2024, 40(9): 1731-1742. doi: 10.11862/CJIC.20240077
6. [6]
  Ling Zhang , Jing Kang . Turn Waste into Valuable: Preparation of High-Strength Water-Based Adhesives from Polymethylmethacrylate Wastes: a Comprehensive Chemical Experiments. University Chemistry, 2024, 39(2): 221-226. doi: 10.3866/PKU.DXHX202306075
7. [7]
  Yunhao Zhang , Yinuo Wang , Siran Wang , Dazhen Xu . Progress in Selective Construction of Functional Aromatics from Nitrogenous Cycloalkanes. University Chemistry, 2024, 39(11): 136-145. doi: 10.3866/PKU.DXHX202401083
8. [8]
  Jiakun BAI , Ting XU , Lu ZHANG , Jiang PENG , Yuqiang LI , Junhui JIA . A red-emitting fluorescent probe with a large Stokes shift for selective detection of hypochlorous acid. Chinese Journal of Inorganic Chemistry, 2024, 40(6): 1095-1104. doi: 10.11862/CJIC.20240002
9. [9]
  Xilin Zhao , Xingyu Tu , Zongxuan Li , Rui Dong , Bo Jiang , Zhiwei Miao . Research Progress in Enantioselective Synthesis of Axial Chiral Compounds. University Chemistry, 2024, 39(11): 158-173. doi: 10.12461/PKU.DXHX202403106
10. [10]
  Zongpei Zhang , Yanyang Li , Yanan Si , Kai Li , Shuangquan Zang . Developing a Chemistry Experiment Center Employing a Multifaceted Approach to Serve High-Quality Laboratory Education. University Chemistry, 2024, 39(7): 13-19. doi: 10.12461/PKU.DXHX202404041
11. [11]
  Jie ZHAO , Sen LIU , Qikang YIN , Xiaoqing LU , Zhaojie WANG . Theoretical calculation of selective adsorption and separation of CO₂ by alkali metal modified naphthalene/naphthalenediyne. Chinese Journal of Inorganic Chemistry, 2024, 40(3): 515-522. doi: 10.11862/CJIC.20230385
12. [12]
  Junjie Zhang , Yue Wang , Qiuhan Wu , Ruquan Shen , Han Liu , Xinhua Duan . Preparation and Selective Separation of Lightweight Magnetic Molecularly Imprinted Polymers for Trace Tetracycline Detection in Milk. University Chemistry, 2024, 39(5): 251-257. doi: 10.3866/PKU.DXHX202311084
13. [13]
  Min Gu , Huiwen Xiong , Liling Liu , Jilie Kong , Xueen Fang . Rapid Quantitative Detection of Procalcitonin by Microfluidics: An Instrumental Analytical Chemistry Experiment. University Chemistry, 2024, 39(4): 87-93. doi: 10.3866/PKU.DXHX202310120
14. [14]
  Xinlong WANG , Zhenguo CHENG , Guo WANG , Xiaokuen ZHANG , Yong XIANG , Xinquan WANG . Enhancement of the fragile interface of high voltage LiCoO₂ by surface gradient permeation of trace amounts of Mg/F. Chinese Journal of Inorganic Chemistry, 2024, 40(3): 571-580. doi: 10.11862/CJIC.20230259
15. [15]
  Yinuo Wang , Siran Wang , Yilong Zhao , Dazhen Xu . Selective Synthesis of Diarylmethyl Anilines and Triarylmethanes via Multicomponent Reactions: Introduce a Comprehensive Experiment of Organic Chemistry. University Chemistry, 2024, 39(8): 324-330. doi: 10.3866/PKU.DXHX202401063
16. [16]
  Ling Bai , Limin Lu , Xiaoqiang Wang , Dongping Wu , Yansha Gao . Exploration and Practice of Teaching Reforms in “Quantitative Analytical Chemistry” under the Perspective of New Agricultural Science. University Chemistry, 2024, 39(3): 158-166. doi: 10.3866/PKU.DXHX202308101
17. [17]
  Xingyang LI , Tianju LIU , Yang GAO , Dandan ZHANG , Yong ZHOU , Meng PAN . A superior methanol-to-propylene catalyst: Construction via synergistic regulation of pore structure and acidic property of high-silica ZSM-5 zeolite. Chinese Journal of Inorganic Chemistry, 2024, 40(7): 1279-1289. doi: 10.11862/CJIC.20240026
18. [18]
  Liang MA , Honghua ZHANG , Weilu ZHENG , Aoqi YOU , Zhiyong OUYANG , Junjiang CAO . Construction of highly ordered ZIF-8/Au nanocomposite structure arrays and application of surface-enhanced Raman spectroscopy. Chinese Journal of Inorganic Chemistry, 2024, 40(9): 1743-1754. doi: 10.11862/CJIC.20240075
19. [19]
  Junke LIU , Kungui ZHENG , Wenjing SUN , Gaoyang BAI , Guodong BAI , Zuwei YIN , Yao ZHOU , Juntao LI . Preparation of modified high-nickel layered cathode with LiAlO₂/cyclopolyacrylonitrile dual-functional coating. Chinese Journal of Inorganic Chemistry, 2024, 40(8): 1461-1473. doi: 10.11862/CJIC.20240189
20. [20]
  Yangrui Xu , Yewei Ren , Xinlin Liu , Hongping Li , Ziyang Lu . 具有高传质和亲和表面的NH₂-UIO-66基疏水多孔液体用于增强CO₂光还原. Acta Physico-Chimica Sinica, 2024, 40(11): 2403032-. doi: 10.3866/PKU.WHXB202403032

Get Citation

PDF

XML

Metrics

PDF Downloads(1160)
Abstract views(2338)
HTML views(13)

通讯作者: 陈斌, bchen63@163.com

1.
沈阳化工大学材料科学与工程学院沈阳 110142