ISSN 1000-6818CN 11-1892/O6CODEN WHXUEU
Acta Phys Chim Sin >> 1998,Vol.14>> Issue(01)>> 1-4     doi: 10.3866/PKU.WHXB19980101         中文摘要
Role of Compound Orientation in CoMFA Studies
Wang Ren-Xiao, Gao Ying, Liu Liang, Lai Lu-Hua
Institute of Physical Chemistry,Peking University,Beijing 100871
Full text: PDF (593KB) HTML Export: BibTeX | EndNote (RIS)

Our work shows that different compound orientations have different results in Comparative Molecular Field Analysis(CoMFA).For three analyzed compound series, the squared correlation coefficients of cross-validation(q2)could vary as largely as 0.30~0.40 among all possible orientations. The reason for this comes from the routine adopted by CoMFA which uses discrete, regularly arrayed grids to represent the molecular field. Therefore, different orientations may map their molecular fields differently onto the grid and accordingly give different results from partial least square (PLS)analyses. We have developed a method all-orientation searching, to seek for the orientation with the best CoMFA result. And ,we suggest that all-orientation searching should be incorporated into the standard CoMFA procedure.

Keywords: CoMFA   All-orientation searching   Determining region  
Received: 1997-07-04 Accepted: 1997-10-24 Publication Date (Web): 1998-01-15
Corresponding Authors: Lai Lu-Hua Email:

Cite this article: 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.    doi: 10.3866/PKU.WHXB19980101
1. LIU Hai-Chun, LU Shuai, RAN Ting, ZHANG Yan-Min, XU Jin-Xing, XIONG Xiao, XU An-Yang, LU Tao, CHEN Ya-Dong.Accurate Activity Predictions of B-Raf Type II Inhibitors via Molecular Docking and QSAR Methods[J]. Acta Phys. -Chim. Sin., 2015,31(11): 2191-2206
2. 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
3. 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
4. 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
5. 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
6. 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
7. 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
8. 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
9. 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
10. 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
11. YAN Lin-Fang, HU Gui-Xiang, XU Jing, ZHAO Wen-Na, YU Qing-Sen.3D-QSAR Models on Cholesteryl Ester Transfer Protein Inhibitors[J]. Acta Phys. -Chim. Sin., 2008,24(12): 2249-2256
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. Lu Ai-Jun;Liu Bing;Liu Hai-Bo;Zhou Jia-Ju.3D-QSAR Study of Benzodiazepines at Five Recombinant GABAA/Benzodiazepine Receptor Subtypes[J]. Acta Phys. -Chim. Sin., 2004,20(05): 488-493
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. Huang Chang-Kang;Gao Ying;Liu Zhen-Ming;Liu Ying;Lai Lu-Hua.Comparative Molecular Field Analysis of Pyrrolidine Inhibitors for Human Cytosolic Phospholipase A2[J]. Acta Phys. -Chim. Sin., 2003,19(01): 79-81
31. Zhu Li-Li;Xu Xiao-Jie.3D-QSAR Analyses of Melatonin Antagonists[J]. Acta Phys. -Chim. Sin., 2002,18(12): 1087-1092
32. 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
33. 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
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, 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
36. 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
37. 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
38. 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
39. Liu Liang,Wang Ren-Xiao,Lai Lu-Hua,Li Chong-Xi.3D-QSAR and Pharmacophore Modeling of Growth Hormone Secretagogues[J]. Acta Phys. -Chim. Sin., 1997,13(12): 1090-1096
40. 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
41. 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
42. 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
43. 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
44. 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
Copyright © 2006-2016 Editorial office of Acta Physico-Chimica Sinica
Address: College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P.R.China
Service Tel: +8610-62751724 Fax: +8610-62756388
^ Top