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ISSN 1000-6818CN 11-1892/O6CODEN WHXUEU
Acta Phys Chim Sin >> 2009,Vol.25>> Issue(08)>> 1587-1592     doi: 10.3866/PKU.WHXB20090752         中文摘要
A Novel QSAR Model Based on Geostatistics and Support Vector Regression
CHEN Yuan, YUAN Zhe-Ming, ZHOU Wei, XIONG Xing-Yao
College of Bio-safety Science and Technology, Hunan AgriculturalUniversity, Changsha 410128, P. R. China|Hunan Provincial Key Laboratory of Crop GermplasmInnovation andUtilization, Hunan AgriculturalUniversity, Changsha 410128, P. R. China
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Based on principal component analysis (PCA), geostatistics (GS) and support vector regression (SVR), a novel individual forecasting method for quantitative structure-activity relationship (QSAR)——Weight-PCA-GS-SVR was proposed. The basic principles were as follows: firstly, dimensions were reduced and redundant information from independent descriptors was eliminated using PCA; secondly, the principal components that have no relationship to activity were removed nonlinearly using SVR; thirdly, weighted distances between samples were calculated by the retained principal components; fourthly, a common range was confirmed using high-dimensional geostatistics; lastly, k nearest neighbors of each test sample were found from the training set with their weighted distances shorter than a common range and then the models were constructed and the individual prediction was found to be feasible using SVR. Weight-PCA-GS-SVR optimized the model along the column direction (descriptor) and row direction (sample), and had all the advantages of SVR. It therefore provides a newway to choose k nearest neighbors in the field as well as being a novel weighted method for determining the retained principal components or the retained descriptors. Predicted results from three data sets all verify that the novel method has the highest prediction precision among all reference models and has a remarkable advantage over reported results. Weight-PCA-GS-SVR, therefore, can be widely used in QSAR and other regression prediction fields.



Keywords: Quantitative structure-activity relationship   Geostatistics   Support vector regression   Principal component analysis   Individual prediction  
Received: 2009-03-16 Accepted: 2009-04-15 Publication Date (Web): 2009-05-26
Corresponding Authors: YUAN Zhe-Ming Email: zhmyuan@sina. com


Cite this article: CHEN Yuan, YUAN Zhe-Ming, ZHOU Wei, XIONG Xing-Yao. A Novel QSAR Model Based on Geostatistics and Support Vector Regression[J]. Acta Phys. -Chim. Sin., 2009,25 (08): 1587-1592.    doi: 10.3866/PKU.WHXB20090752
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4. SUN Sang-Dun, MI Si-Qi, YOU Jing, YU Ji-Liang, HU Song-Qing, LIU Xin-Yong.HQSAR Study and Molecular Design of Benzimidazole Derivatives as Corrosion Inhibitors[J]. Acta Phys. -Chim. Sin., 2013,29(06): 1192-1200
5. WANG Zhi-Ming, HAN Na, YUAN Zhe-Ming, WU Zhao-Hua.Feature Selection for High-Dimensional Data Based on Ridge Regression and SVM and Its Application in Peptide QSAR Modeling[J]. Acta Phys. -Chim. Sin., 2013,29(03): 498-507
6. KANG Cong-Min, ZHAO Xu-Hao, WANG Xin-Yu, CHENG Jia-Gao, LÜ Ying-Tao.QSAR and Molecular Docking on Five-Membered Heterocyclopyrimidines as Thymidylate Synthase Inhibitors[J]. Acta Phys. -Chim. Sin., 2013,29(02): 431-438
7. TAO Wan-Jun, LI Chen-Wen, YIN Zong-Ning.Design of Self-Emulsifying System Based on QSAR[J]. Acta Phys. -Chim. Sin., 2011,27(01): 71-77
8. DUAN Hong-Xia, WANG Rui-Gang, ZHANG Jian-Jun, DONG Yan-Hong, LIANG Xiao-Mei, WU Jing-Ping, WANG Dao-Quan.QSAR of Macrolactone Derivatives with Herbicidal Activity[J]. Acta Phys. -Chim. Sin., 2010,26(04): 1065-1074
9. HU Song-Qing, HU Jian-Chun, SHI Xin, ZHANG Jun, GUO Wen-Yue.QSAR and Molecular Design of Imidazoline Derivatives as Corrosion Inhibitors[J]. Acta Phys. -Chim. Sin., 2009,25(12): 2524-2530
10. WEI Zhuo, ZHANG Huai, CUI Wei, JI Ming-Juan.Molecular Docking and 3D-QSAR on Maleimide Derivatives as Glycogen Synthase Kinase-3β Inhibitors[J]. Acta Phys. -Chim. Sin., 2009,25(05): 890-896
11. MEI Hu, LIU Li, YANG Li, LI Jian, YAN Ning, WANG Qin.Prediction of Antitumor Activities of Indolo[1,2-b]Quinazoline Derivatives Using Electrotopological State Indices for AtomTypes[J]. Acta Phys. -Chim. Sin., 2009,25(04): 747-751
12. JIANG Yu-Ren; QIN Wei.3D-QSAR Analysis on Benzoxazinone Derivatives[J]. Acta Phys. -Chim. Sin., 2008,24(10): 1859-1863
13. FENG Chang-Jun; MU Lai-Long; YNAG Wei-Hua; CAI Ke-Ying.A Mathematical Model between Bioconcentration Factors and Topological Indices of Organic Pollutants[J]. Acta Phys. -Chim. Sin., 2008,24(06): 1053-1057
14. SONG Zhe;LIU Tao;LIU Wei;ZHU Ming-Hua;WANG Xiao-Gang .The QSAR Model Study of Interaction Between Peptides and MHC molecules[J]. Acta Phys. -Chim. Sin., 2007,23(02): 198-205
15. TONG Jian-Bo;ZHANG Sheng-Wan.A New 3D-Descriptor of Amino Acids and Its Application in Quantitative Structure Activity Relationship of Peptide Drugs[J]. Acta Phys. -Chim. Sin., 2007,23(01): 37-43
16. TONG Jian-Bo;ZHOU Peng;ZHANG Sheng-Wan;LIANG Gui-Zhao;TIAN Fei-Fei;LI Mei-Ping;LI Sheng-Shi.QSAR Studies of Anti-HIV Drug HEPT Using 3D-HoVAIF[J]. Acta Phys. -Chim. Sin., 2006,22(06): 721-725
17. ZHOU Yuan;MEI Hu;LIANG Gui-Zhao;LI Zhi-Liang.Physicochemical Parameters of Substituents and Its Application in Quantitative Structure Activity Relationship for Drugs[J]. Acta Phys. -Chim. Sin., 2006,22(04): 486-491
18. LIANG Gui-Zhao; MEI Hu; ZHOU Peng; ZHOU Yuan; LI Zhi-Liang.Study on Quantitative Structure-Activity Relationship by 3D Holographic Vector of Atomic Interaction Field[J]. Acta Phys. -Chim. Sin., 2006,22(03): 388-390
19. QIAO Ying-xin; ZHOU Jia-ju.A 3D-QSAR Study with Energy of Molecular Orbitals on N-Aminoidazoles[J]. Acta Phys. -Chim. Sin., 2006,22(02): 209-214
20. SHEN Bin; LU Zhong-hua; CHI Xue-bin; LÜ Hai-feng; REN Tian-rui.Research on Pseudoreceptor Models for the Inhibitors at GABA Receptors via Flexible Atom Receptor Model[J]. Acta Phys. -Chim. Sin., 2005,21(07): 800-803
21. HUANG Qin; HOU Ting -Jun; XU Xiao-Jie.The Prediction of Caco-2 Permeation Based on Genetic Algorithm[J]. Acta Phys. -Chim. Sin., 2005,21(04): 372-377
22. WU Wen-Juan;LAI Rong;ZHENG Kang-Cheng;YUN Feng-Cun.Quantitative Structure-Activity Relationship of Indolo[1,2-b]quinazoline Derivatives with Antitumor Activity[J]. Acta Phys. -Chim. Sin., 2005,21(01): 28-32
23. Mei Hu;Zhou Yuan;Sun Li-Li;Li Zhi-Liang.A New Descriptor of Amino Acids and Its Application in Peptide QSAR[J]. Acta Phys. -Chim. Sin., 2004,20(08): 821-825
24. Wang Bao-Lei;Ma Ning;Wang Jian-Guo;Ma Yi;Li Zheng-Ming;Li Yong-Hong.3D-QSAR Analysis of New Sulfonylureas Related to Their Herbicidal Activity[J]. Acta Phys. -Chim. Sin., 2004,20(06): 577-581
25. Hu Gui-Xiang;Zou Jian-Wei;Jiang Yong-Jun;Wang Yan-Hua;Yu Qing-Sen.Predicting Human Intestinal Absorption from Threedimensional Molecular Structure of Drugs[J]. Acta Phys. -Chim. Sin., 2004,20(05): 512-517
26. Ding Jun-Jie;Ding Xiao-Qin;Zhao Li-Feng;Chen Ji-Sheng.Three Dimensional Quantitative Structure-activity Relationship of Dihydropyridine Derivatives[J]. Acta Phys. -Chim. Sin., 2003,19(12): 1108-1113
27. Pan Yong-Mei;Ji Ming-Juan.Applications of Genetic Algorithms on 2D-QSAR Analysis of Benzofuran and Benzothiophene Biphenyls as PTP1B Inhibitors[J]. Acta Phys. -Chim. Sin., 2003,19(08): 695-700
28. Zhang Hua-Bei;Li Bo;Dai Mei.QSAR of [99Tcm(NO)Cl(PL)2] Complexes[J]. Acta Phys. -Chim. Sin., 2003,19(05): 460-463
29. Peng Tao;Pei Jian-Feng;Zhou Jia-Ju.Three-dimensional Quantitative Structure-Activity Relationship Study of Tyrosine Kinase Inhibitors[J]. Acta Phys. -Chim. Sin., 2003,19(02): 163-166
30. Zhu Li-Li;Xu Xiao-Jie.3D-QSAR Analyses of Melatonin Antagonists[J]. Acta Phys. -Chim. Sin., 2002,18(12): 1087-1092
31. Zou Xia-Juan;Lai Lu-Hua;Jin Gui-Yu;Huang Gui-Qin.Studies on the 3D-QSAR of Novel 1-aryl-1,4-dihydro-3-acylhydrazinocarbonyl-6-methyl- 4-pyridazinones[J]. Acta Phys. -Chim. Sin., 2002,18(06): 513-516
32. Yang Guang-Fu, Liu Hua-Yin, Yang Xiu-Feng, Yang Hua-Zheng.CoMFA Studies on Herbicidal 1,2,4-Triazolo[1,5-a]pyrimidine-2-Sulfonanilides[J]. Acta Phys. -Chim. Sin., 1999,15(02): 190-192
33. Wang Ren-Xiao, Feng Ya-Bin, Lai Lu-Hua, Tang You-Qi.Structure-Affinity Relationship of lndole-Based for Phospholipase A2[J]. Acta Phys. -Chim. Sin., 1998,14(10): 893-897
34. Wang Ren-Xiao, Liu Liang, Lai Lu-Hua, Tang You-Qi.Structure-Affinity Relationship of Thrombin inhibitors[J]. Acta Phys. -Chim. Sin., 1998,14(10): 887-892
35. Wang Ren-Xiao, Li Wei-Zhong, Lai Lu-Hua, Tang You-Qi.Estimating Binding Affinities for Enzyme-Ligand Complexes[J]. Acta Phys. -Chim. Sin., 1998,14(09): 826-832
36. Huang Zhong-Ping, Pan Jin-Hong, Cai Guo-Qiang, Yu Qing-Sen, Lin Rui-Sen.Study on the Structure-Photosensitivity Relationship of Bis(4-dimethylaminophenyl)squaraine Derivatives[J]. Acta Phys. -Chim. Sin., 1998,14(06): 557-561
37. Wang Jin-Ling, Sun Ming, Su Hua-Qing, Miao Fang-Ming.3D-Quantitative Structure-Activity Relationship Studies of Imidazole-1-carboxylates[J]. Acta Phys. -Chim. Sin., 1998,14(05): 444-447
38. Wang Ren-Xiao, Gao Ying, Liu Liang, Lai Lu-Hua.Role of Compound Orientation in CoMFA Studies[J]. Acta Phys. -Chim. Sin., 1998,14(01): 1-4
39. Chen Hong-Ming,Zhou Jia-Ju,Xie Gui-Rong,Ren Tian-Rui.A QSAR Research Method Based on Pseudoreceptor Model[J]. Acta Phys. -Chim. Sin., 1997,13(07): 626-631
40. Zhu Long-Guan, Yu Qing-Sen, Chen Kai-Xian, Cai Cuo-Qiang, Lin Rui-Sen.Study on the Quantitative Structure-activity Relationship of N1 Position of Quinolone[J]. Acta Phys. -Chim. Sin., 1995,11(10): 925-928
41. Luo Zhao-Wen, Wang Dan-Dan, Lai Lu-Hua, Xu Xiao-Jia, Li Chong-Xi.3D-QSAR Studies of Galanthamine and Analogs[J]. Acta Phys. -Chim. Sin., 1995,11(05): 419-423
42. Feng Jun, Zhou Jia-Ju, Li Ren-Li.Comparative Molecular Field Analysis of Inotropic Compounds and Pyridazinone[J]. Acta Phys. -Chim. Sin., 1995,11(03): 206-210
43. LIN Feng, FU Xin-Mei, WANG Chao, JANG Si-Yu, WANG Jing-Hui, ZHANG Shu-Wei, YANG Ling, LI Yan.QSAR, Molecular Docking and Molecular Dynamics on 3C-like Protease Inhibitors[J]. Acta Phys. -Chim. Sin., 0,(): 0-0
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