Modeling Enzyme-phage Peptide Recognition——Docking Method Based on Surface Electrostatic Complementary and Solvation Energy

Chem. J. Chinese Universities ›› 2000, Vol. 21 ›› Issue (11): 1703.

• Articles • Previous Articles Next Articles

Modeling Enzyme-phage Peptide Recognition——Docking Method Based on Surface Electrostatic Complementary and Solvation Energy

LI Fei¹, WANG Yu-Hong², LI Wei², ZHOU Hui², MAO You-Gang¹, SHEN Jia-Cong¹

1. Key Laboratory of Supramolecular Structure and Spectroscopy, Educational Ministry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023;
2. Departmentof Molecular Biology, Collegeof Life Science, Jilin University, Changchun 130023, China

Received:1999-09-15 Online:2000-11-24 Published:2000-11-24

Abstract

Abstract: A novel Docking algorithm is presented which combines a simple electrostatic complementary model with a solvation energy model. A computer program ESCOLD(Electro Static Complementary Optimization for Ligand Docking) has been developed for Docking of phage peptide to a target enzyme. In three test cases where the phage peptides(with six amide residues binding to enzyme) of X-ray crystallographically determined complexes are redocked, the family of the orientations closest to the experimental binding geometry was correctly identified with the solvation energy score.

Key words: Enzyme-phage peptide, Docking, Surface electrostatic complementary, Solvation energy

CLC Number:

O641.3

TrendMD:

LI Fei, WANG Yu-Hong, LI Wei, ZHOU Hui, MAO You-Gang, SHEN Jia-Cong . Modeling Enzyme-phage Peptide Recognition——Docking Method Based on Surface Electrostatic Complementary and Solvation Energy[J]. Chem. J. Chinese Universities, 2000, 21(11): 1703.

[1]	LEI Xiaotong, JIN Yiqing, MENG Xuanyu. Prediction of the Binding Site of PIP₂ in the TREK-1 Channel Based on Molecular Modeling [J]. Chem. J. Chinese Universities, 2021, 42(8): 2550.
[2]	SHUAI Die, ZHAO Meijuan, CHEN Bingnian, WANG Li. Inhibitory Effect of Four Kinds of Keegin-type Phosphomolybdate on Tyrosinase and Melanin Formation and Its Antioxidant Activities [J]. Chem. J. Chinese Universities, 2021, 42(12): 3579.
[3]	YANG Ju, SU Lijiao, LI Canhua, LU Jiajia, YANG Junli, GU Jie, YANG Li, YANG Lijuan. Host-guest Complexation Behavior of Nardosinone and Water-soluble Phosphate Salt Pillar［6］arene [J]. Chem. J. Chinese Universities, 2021, 42(10): 3099.
[4]	ZHANG Aiqin, WANG Man, SHEN Gangyi, JIN Jun. Interactions Between Polybrominated Diphenyl Ethers and Human Serum Albumin Using SPR and Molecular Docking [J]. Chem. J. Chinese Universities, 2020, 41(9): 2054.
[5]	WANG Lianping,LI Qingjie,LIU Xiaoyan,REN Yueying,YANG Xiuwei. Screening of Cholinesterase Inhibitors in Fructus Evodiae Alkaloids Based on UFLC-MS/molecular Simulation ^† [J]. Chem. J. Chinese Universities, 2020, 41(1): 111.
[6]	WANG Xiaoxia, MA Litong, NIE Zhihua, WANG Zhengde, CUI Jinlong, ZHAO Wenyuan, SAI Huazheng. Interaction Between Fulvic Acid and Pepsin Investigated by Multispectral and Molecular Docking Simulation ^† [J]. Chem. J. Chinese Universities, 2019, 40(9): 1840.
[7]	LIU Zhongcheng, LIU Shifang, ZHANG Su, YANG Yanlei, LI Fei, ZHANG Nan, YUAN Xin, ZHANG Yanfen. Structure Prediction and Screening of Oligonucleotide Aptamers Target Cε3-Cε4 Protein^† [J]. Chem. J. Chinese Universities, 2019, 40(1): 83.
[8]	XIN Meiling, CHU Zhenhua, LI Yu. Molecular Modification of Polychlorinated Biphenyl Dihydroxy Derivatives Through Molecular Docking Associated with CoMSIA/HQSAR Models^† [J]. Chem. J. Chinese Universities, 2018, 39(2): 299.
[9]	WANG Yan, CHEN Ping, WANG Yunfei, LIU Guiying, YANG Xi, SU Ying, LI Junyang, LIU Weiwei, LIN Lie. Spectral Characterization of the Interaction Between Methamphetamine and Serum Albumin^† [J]. Chem. J. Chinese Universities, 2018, 39(11): 2507.
[10]	DUAN Yongbin, YIN Yan, MENG Fanli, ZHAO Lianhua, LIU Yukun, YUAN Zhe, FENG Yangbo. Design, Synthesis and Biological Evaluation of Benzothiazoles as Highly Potent ROCK Inhibitors Through Molecular Docking and Free Energy Calculations^† [J]. Chem. J. Chinese Universities, 2017, 38(9): 1568.
[11]	WANG Song, GUAN Shanshan, WAN Yongfeng, SHAN Yaming, ZHANG Hao. Molecular Dynamics Simulation Study on the Binding Modes of Angiotensin-converting Enzyme with Inhibitory Peptides^† [J]. Chem. J. Chinese Universities, 2017, 38(7): 1216.
[12]	TANG Qian, SU Jinhong, CAO Hongyu, WANG Lihao, SHI Fei, WANG Ailing, GONG Tingting, JIN Xiaojun, ZHENG Xuefang. Interaction of Pyrimidine Derivatives with Human Serum Albumin^† [J]. Chem. J. Chinese Universities, 2017, 38(11): 1982.
[13]	ZHAO Bin, HUO Jingqian, XING Jihong, QI Meng, ZHANG Jinlin, DONG Jingao. Homologous Modeling of Transketolase AtTKL1 and Its Combination with α-Terthienyl in Arabidopsis Thaliana^† [J]. Chem. J. Chinese Universities, 2015, 36(4): 682.
[14]	DONG Lu, YI Zhongsheng, WU Zhiwei, WANG Haiyang, ZHANG Aiqian. Mechanism Study on the Interaction Between 2'-Hydroxy-2,4-dibromo Diphenyl Ethers and Human Serum Albumin Based on Spectroscopic Methods and Computional Simulations^† [J]. Chem. J. Chinese Universities, 2015, 36(3): 516.
[15]	ZHANG Min, ZHANG Yi, LI Chengtao, QIN Jiaxiang, Gao Rang, MA Xiaoning, QIU Jianhui. N435 Enzymatic Degradation Difference and Molecular Modeling of Hydrophilic Modified PBS-based Copolymer^† [J]. Chem. J. Chinese Universities, 2015, 36(3): 568.

Modeling Enzyme-phage Peptide Recognition——Docking Method Based on Surface Electrostatic Complementary and Solvation Energy

PDF (PC)

Knowledge

Abstract

Cite this article

share this article

References

Related Articles 15

Recommended Articles

Metrics

Comments