蛋白质-蛋白质分子对接中打分函数研究进展

doi:10.3866/PKU.WHXB201202022

物理化学学报 >> 2012, Vol. 28 >> Issue (04): 751-758.doi: 10.3866/PKU.WHXB201202022

蛋白质-蛋白质分子对接中打分函数研究进展

王存新¹, 常珊², 龚新奇³, 杨峰¹, 李春华¹, 陈慰祖¹

1. 北京工业大学生命科学与生物工程学院, 北京 100124;
2. 华南农业大学信息学院, 广州 510642;
3. 清华大学生命科学学院, 北京100084

收稿日期:2011-11-22 修回日期:2012-01-12 发布日期:2012-03-21
通讯作者: 王存新 E-mail:cxwang@bjut.edu.cn
基金资助:
国家自然科学基金(10974008, 31171267), 教育部博士点基金项目(200800050003)和科技部国际合作项目(2010DFA31710)资助

Progress in the Scoring Functions of Protein-Protein Docking

WANG Cun-Xin¹, CHANG Shan², GONG Xin-Qi³, YANG Feng¹, LI Chun-Hua¹, CHEN Wei-Zu¹

1. College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, P. R. China;
2. College of Informatics, South China Agricultural University, Guangzhou 510642, P. R. China;
3. School of Life Sciences, Tsinghua University, Beijing 100084, P. R. China

Received:2011-11-22 Revised:2012-01-12 Published:2012-03-21
Contact: WANG Cun-Xin E-mail:cxwang@bjut.edu.cn
Supported by:
The project was supported by the National Natural Science Foundation of China (10974008, 31171267), Specialized Research Fund for the Doctoral Program of Higher Education, China (200800050003), and International Science & Technology Cooperation Program of China (2010DFA31710).

摘要/Abstract

摘要： 分子对接是研究分子间相互作用与识别的有效方法. 其中, 用于近天然构象挑选的打分函数的合理设计对于对接中复合物结构的成功预测至关重要. 本文回顾了蛋白质-蛋白质分子对接组合打分函数中一些主要打分项, 包括几何互补项、界面接触面积、范德华相互作用能、静电相互作用能以及统计成对偏好势等打分项的计算方法. 结合本研究小组的工作, 介绍了目前普遍使用的打分方案以及利用与结合位点有关的信息进行结构筛选的几种策略, 比较并总结了常用打分函数的特点. 最后, 分析并指出了当前蛋白质-蛋白质对接打分函数所存在的主要问题, 并对未来的工作进行了展望.

关键词: 蛋白质-蛋白质分子对接, 打分函数, 打分策略, 结合位点信息

Abstract: Molecular docking technology is an effective approach for prediction of intermolecular interactions and recognition. The design of a scoring function for selecting near-native structures is very important for successful prediction of complex structures. In this article, the main computational methods for scoring items in protein-protein docking, such as geometric complementarity, contact area, van der Waals' interaction, electrostatic interaction, and statistical pair propensity potential, are reviewed. Including our work, we introduce commonly used scoring schemes and some strategies in screening decoys based on the information for protein binding sites. The characteristic scoring functions in the commonly used docking programs are compared and summarized. The major problems in the existing scoring function in protein-protein docking are discussed along with prospect for future research.

Key words: Protein-protein docking, Scoring function, Scoring scheme, Binding site information

王存新, 常珊, 龚新奇, 杨峰, 李春华, 陈慰祖. 蛋白质-蛋白质分子对接中打分函数研究进展[J]. 物理化学学报, 2012, 28(04), 751-758. doi: 10.3866/PKU.WHXB201202022

WANG Cun-Xin, CHANG Shan, GONG Xin-Qi, YANG Feng, LI Chun-Hua, CHEN Wei-Zu. Progress in the Scoring Functions of Protein-Protein Docking[J]. Acta Phys. -Chim. Sin. 2012, 28(04), 751-758. doi: 10.3866/PKU.WHXB201202022

链接本文: https://www.whxb.pku.edu.cn/CN/10.3866/PKU.WHXB201202022

https://www.whxb.pku.edu.cn/CN/Y2012/V28/I04/751

参考文献

(1) Pearson, H. Nature 2008, 452, 920.

(2) Hummon, A. B.; Richmond, T. A.; Verleyen, P.; Baggerman, G.; Huybrechts, J.; Ewing, M. A.; Vierstraete, E.; Rodriguez-Zas, S. L.; Schoofs, L.; Robinson, G. E.; Sweedler, J. V. Science 2006, 314, 647.

(3) Phizicky, E.; Bastiaens, P. I. H.; Zhu, H.; Snyder, M.; Fields, S. Nature 2003, 422, 208.

(4) Moreira, I. S.; Fernandes, P. A.; Ramos, M. J. J. Comput. Chem. 2010, 31, 317.
(5) Ritchie, D.W. Curr. Protein Pept. Sci. 2008, 9, 1.

(6) Gray, J. J. Curr. Opin. Struct. Biol. 2006, 16, 183.

(7) Li, C. H.; Ma, X. H.; Chen,W. Z.;Wang, C. X. Progress in Biochemistry and Biophysics 2006, 33, 616. [李春华, 马晓慧, 陈慰祖, 王存新. 生物化学与生物物理进展, 2006, 33, 616.]
(8) Li, X. D.; Hou, T. J.; Xu, X. J. Acta Physico-Chimica Sinica 2005, 21, 504. [李旭东, 侯廷军, 徐筱杰. 物理化学学报, 2005, 21, 504.]
(9) Janin, J.; Henrick, K.; Moult, J.; Ten Eyck, L.; Sternberg, M. J. E.; Vajda, S.; Vasker, I.;Wodak, S. J. Proteins 2003, 52, 2.

(10) Mendez, R.; Leplae, R.; Lensink, M. F.;Wodak, S. J. Proteins 2005, 60, 150.

(11) Janin, J. Mol. Biosyst. 2010, 6, 2351.

(12) Katchalski-Katzir, E.; Shariv, I.; Eisenstein, M.; Friesem, A. A.; Aflalo, C.; Vakser, I. A. Proc. Natl. Acad. Sci. U. S. A. 1992, 89, 2195.

(13) Chen, R.; Li, L.;Weng, Z. P. Proteins 2003, 52, 80.

(14) Mandell, J. G.; Roberts, V. A.; Pique, M. E.; Kotlovyi, V.; Mitchell, J. C.; Nelson, E.; Tsigelny, I.; Ten Eyck, L. F. Protein Eng. 2001, 14, 105.

(15) Aloy, P.; Querol, E.; Aviles, F. X.; Sternberg, M. J. E. J. Mol. Biol. 2001, 311, 395.

(16) Fischer, D.; Lin, S. L.;Wolfson, H. L.; Nussinov, R. J. Mol. Biol. 1995, 248, 459.
(17) Schneidman-Duhovny, D.; Inbar, Y.; Nussinov, R.;Wolfson, H. J. Nucl. Acids Res. 2005, 33,W363.

(18) Venkatraman, V.; Yang, Y. F. D.; Sael, L.; Kihara, D. BMC Bioinformatics 2009, 10, 407.

(19) Li, N.; Sun, Z.; Jiang, F. Proteins 2007, 69, 801.

(20) Li, C. H.; Ma, X. H.; Chen,W. Z.;Wang, C. X. Proteins 2003, 52, 47.

(21) Chakrabarti, P.; Janin, J. Proteins 2002, 47, 334.

(22) Gardiner, E. J.;Willett, P.; Artymiuk, P. J. Proteins 2003, 52, 10.

(23) Kuntz, I. D.; Chen, K.; Sharp, K. A.; Kollman, P. A. Proc. Natl. Acad. Sci. U. S. A. 1999, 96, 9997.

(24) Fernandez-Recio, J.; Totrov, M.; Abagyan, R. J. Mol. Biol. 2004, 335, 843.

(25) Gray, J. J.; Moughon, S.;Wang, C.; Schueler-Furman, O.; Kuhlman, B.; Rohl, C. A.; Baker, D. J. Mol. Biol. 2003, 331, 281.

(26) Hou, T. J.; Xu, X. J. Acta Physico-Chimica Sinica 2002, 18, 1052. [侯廷军, 徐筱杰. 物理化学学报, 2002, 18, 1052.]
(27) Li, L.; Guo, D.; Huang, Y.; Liu, S.; Xiao, Y. BMC Bioinformatics 2011, 12, 36.

(28) Anthony, N.; Barry, H. J. Comput. Chem. 1991, 12, 435.

(29) Nicholls, A.; Sharp, K. A.; Honig, B. Proteins 1991, 11, 281.

(30) Madura, J. D.; Briggs, J. M.;Wade, R. C.; Davis, M. E.; Luty, B. A.; Ilin, A.; Antosiewicz, J.; Gilson, M. K.; Bagheri, B.; Scott, L. R.; McCammon, J. A. Comput. Phys. Commun. 1995, 91, 57.

(31) Palma, P. N.; Krippahl, L.;Wampler, J. E.; Moura, J. J. G. Proteins 2000, 39, 372.

(32) Case, D. A.; Cheatham, T. E.; Darden, T.; Gohlke, H.; Luo, R.; Merz, K. M.; Onufriev, A.; Simmerling, C.;Wang, B.;Woods, R. J. J. Comput. Chem. 2005, 26, 1668.

(33) Moont, G.; Gabb, H. A.; Sternberg, M. J. E. Proteins 1999, 35, 364.

(34) Mintseris, J.; Pierce, B.;Wiehe, K.; Anderson, R.; Chen, R.; Weng, Z. P. Proteins 2007, 69, 511.

(35) Vreven, T.; Hwang, H.;Weng, Z. P. Protein Sci. 2011, 20, 1576.

(36) Kozakov, D.; Brenke, R.; Comeau, S. R.; Vajda, S. Proteins 2006, 65, 392.

(37) Zhang, C.; Liu, S.; Zhu, Q.; Zhou, Y. J. Med. Chem. 2005, 48, 2325.

(38) Vajda, S.; Kozakov, D. Curr. Opin. Struct. Biol. 2009, 19, 164.

(39) Charifson, P. S.; Corkery, J. J.; Murcko, M. A.;Walters,W. P. J. Med. Chem. 1999, 42, 5100.

(40) Terp, G. E.; Johansen, B. N.; Christensen, I. T.; Jorgensen, F. S. J. Med. Chem. 2001, 44, 2333.

(41) Li, C. H.; Ma, X. H.; Shen, L. Z.; Chang, S.; Chen,W. Z.; Wang, C. X. Biophys. Chem. 2007, 129, 1.

(42) Gong, X. Q.; Chang, S.; Zhang, Q. H.; Li, C. H.; Shen, L. Z.; Ma, X. H.;Wang, M. H.; Liu, B.; He, H. Q.; Chen,W. Z.; Wang, C. X. Proteins 2007, 69, 859.

(43) Chang, S.; Gong, X. Q.; Jiao, X.; Li, C. H.; Chen,W. Z.;Wang, C. X. Chin. Sci. Bull. 2010, 55, 814.

(44) Chang, S.; Jiao, X.; Li, C. H.; Gong, X. Q.; Chen,W. Z.;Wang, C. X. Biophys. Chem. 2008, 134, 111.

(45) Chen, R.; Mintseris, J.; Janin, J.;Weng, Z. P. Proteins 2003, 52, 88.

(46) Gong, X.;Wang, P.; Yang, F.; Chang, S.; Liu, B.; He, H.; Cao, L.; Xu, X.; Li, C.; Chen,W.;Wang, C. Proteins 2010, 78, 3150.

(47) Camacho, C. J.; Gatchell, D.W.; Kimura, S. R.; Vajda, S. Proteins 2000, 40, 525.

(48) Wang, J.; Morin, P.;Wang,W.; Kollman, P. A. J. Am. Chem. Soc. 2001, 123, 5221.

(49) Bai, H. J.; Lai, L. H. Acta Physico-Chimica Sinica 2010, 26, 1988. [白红军, 来鲁华. 物理化学学报, 2010, 26, 1988.]
(50) Zhang, C.; Liu, S.; Zhou, Y. Q. Proteins 2005, 60, 314.

(51) Heuser, P.; Bau, D.; Benkert, P.; Schomburg, D. Proteins 2005, 61, 1059.

(52) Hu, Z. J.; Ma, B. Y.;Wolfson, H.; Nussinov, R. Proteins 2000, 39, 331.

(53) Dominguez, C.; Boelens, R.; Bonvin, A. J. Am. Chem. Soc. 2003, 125, 1731

(54) Lensink, M. F.;Wodak, S. J. Proteins 2010, 78, 3073.

(55) Ma, X. H.; Li, C. H.; Shen, L. Z.; Gong, X. Q.; Chen,W. Z.; Wang, C. X. Proteins 2005, 60, 319.

(56) Zhou, H. X.; Qin, S. B. Bioinformatics 2007, 23, 2203.

(57) Lichtarge, O.; Bourne, H. R.; Cohen, F. E. J. Mol. Biol. 1996, 257, 342.

(58) Bradford, J. R.;Westhead, D. R. Bioinformatics 2005, 21, 1487.

(59) Gutteridge, A.; Bartlett, G. J.; Thornton, J. M. J. Mol. Biol. 2003, 330, 719.

(60) Wang, C.; Schueler-Furman, O.; Baker, D. Protein Sci. 2005, 14, 1328.

(61) Pierce, B.;Weng, Z. Proteins 2007, 67, 1078
(62) Li, L.; Chen, R.;Weng, Z. Proteins 2003, 53, 693.

(63) Pierce, B.;Weng, Z. Proteins 2008, 72, 270.

(64) Bonvin, A. M. Curr. Opin. Struct. Biol. 2006, 16, 194.

(65) Andrusier, N.; Mashiach, E.; Nussinov, R.;Wolfson, H. J. Proteins 2008, 73, 271.

(66) Sukhwani, B.; Herbordt, M. C. IET Comput. Digit. Tech. 2010, 4, 184.

(67) Dynerman, D.; Butzlaff, E.; Mitchell, J. C. J. Comput. Biol. 2009, 16, 523.

(68) Korb, O.; Stutzle, T.; Exner, T. E. J. Chem Inf. Model. 2011, 51, 865.

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蛋白质-蛋白质分子对接中打分函数研究进展

Progress in the Scoring Functions of Protein-Protein Docking

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