蛋白质-RNA相互作用界面预测与设计

doi:10.3866/PKU.WHXB201209111

Abstract

Abstract:

RNA-protein interactions play key roles in many biological processes. The three dimensional (3D) structure of protein-RNA complexes can be determined experimentally by structural biologists. The recognition between protein and RNA can be understood from the 3D atomic structure. However, the structure determination of protein-RNA complexes by experimental methods is often difficult and costly, and limited to the binding strength. Thus, the prediction and design of protein-RNA complex structures is important in biological medical research. In this review, we will discuss the recent progress in protein-RNA interface prediction and design, which includes the following aspects: (1) protein-RNA docking and the conformational change on binding; (2) the recognition mechanism of protein-RNA binding; (3) the molecular design based on the protein-RNA interface. Improvement of the protein-RNA docking algorithm will help us annotate a large number of proteins and RNA with unknown function, and molecular design based on macromolecular interactions will be useful in drug design.

Key words: Protein-RNA interaction, Molecular docking, Interface design, Complex structure prediction

MSC2000:

O641

HUANG Yang-Yu, YANG Xiu-Feng, LI Hao-Tian, JI Xiao-Feng, CHENG Hong-Li, ZHAO Yun-Jie, GUO Da-Chuan, LI Lin, LIU Shi-Yong. Protein-RNA Interaction Interface Prediction and Design[J].Acta Phys. -Chim. Sin., 2012, 28(10): 2390-2400.

References

(1) Gilbert,W. Nature 1986, 319, 618.
(2) Zhang,W.; Ye, K. Q. Chinese Bulletin of Life Sciences 2010, 22,608. [张炜, 叶克穷. 生命科学, 2010, 22, 608.]
(3) Zhao, S.; Liu, M. F. Chinese Bulletin of Life Sciences 2010, 22,623. [赵爽, 刘默芳. 生命科学, 2010, 22, 623.]
(4) Shao,W.; Fan, Y. J.; Xu, Y. Z. Chinese Bulletin of Life Sciences2010, 22, 711. [邵伟, 樊玉杰, 徐永镇. 生命科学, 2010, 22,711.]
(5) Chen, R. S. Sci. China Life Sci. 2010, 22, 594. [陈润生. 生命科学, 2010, 22, 594.]
(6) Zheng, L. L.; Qu, L. H. Chinese Bulletin of Life Sciences 2010,40, 294. [郑凌伶, 屈良鹄. 中国科学生命科学, 2010, 40,294.]
(7) Liu, M. F.;Wang, E. D. Chinese Bulletin of Life Sciences 2008,20, 178. [刘默芳, 王恩多. 生命科学, 2008, 20, 178.]
(8) Licatalosi, D. D.; Mele, A.; Fak, J. J.; Ule, J.; Kayikci, M.; Chi,S.W.; Clark, T. A.; Schweitzer, A. C.; Blume, J. E.;Wang, X.;Darnell, J. C.; Darnell, R. B. Nature 2008, 456, 464. doi: 10.1038/nature07488
(9) Yang, J. H.; Li, J. H.; Shao, P.; Zhou, H.; Chen, Y. Q.; Qu, L. H.Nucleic Acids Research 2011, 39, D202.
(10) Wu, T.;Wang, J.; Liu, C.; Zhang, Y.; Shi, B.; Zhu, X.; Zhang,Z.; Skogerbo, G.; Chen, L.; Lu, H.; Zhao, Y.; Chen, R. Nucleic Acids Research 2006, 34, D150.
(11) Lunde, B. M.; Moore, C.; Varani, G. Nature Reviews. Molecular Cell Biology 2007, 8, 479. doi: 10.1038/nrm2178
(12) Clery, A.; Blatter, M.; Allain, F. H. Current Opinion in Structural Biology 2008, 18, 290. doi: 10.1016/j.sbi.2008.04.002
(13) Maris, C.; Dominguez, C.; Allain, F. H. The FEBS Journal2005, 272, 2118. doi: 10.1111/j.1742-4658.2005.04653.x
(14) Chen, Y.; Varani, G. The FEBS Journal 2005, 272, 2088. doi: 10.1111/ejb.2005.272.issue-9
(15) Antson, A. A.; Dodson, E. J.; Dodson, G.; Greaves, R. B.; Chen,X.; Gollnick, P. Nature 1999, 401, 235. doi: 10.1038/45730
(16) Frazao, C.; McVey, C. E.; Amblar, M.; Barbas, A.; Vonrhein, C.;Arraiano, C. M.; Carrondo, M. A. Nature 2006, 443, 110. doi: 10.1038/nature05080
(17) Hudson, B. P.; Martinez-Yamout, M. A.; Dyson, H. J.;Wright, P.E. Nature Structural & Molecular Biology 2004, 11, 257. doi: 10.1038/nsmb738
(18) Lewis, H. A.; Musunuru, K.; Jensen, K. B.; Edo, C.; Chen, H.;Darnell, R. B.; Burley, S. K. Cell 2000, 100, 323. doi: 10.1016/S0092-8674(00)80668-6
(19) Lu, D.; Searles, M. A.; Klug, A. Nature 2003, 426, 96. doi: 10.1038/nature02088
(20) Ma, J. B.; Ye, K.; Patel, D. J. Nature 2004, 429, 318. doi: 10.1038/nature02519
(21) Ma, J. B.; Yuan, Y. R.; Meister, G.; Pei, Y.; Tuschl, T.; Patel, D.J. Nature 2005, 434, 666. doi: 10.1038/nature03514
(22) Oberstrass, F. C.; Lee, A.; Stefl, R.; Janis, M.; Chanfreau, G.;Allain, F. H. Nature Structural & Molecular Biology 2006, 13,160. doi: 10.1038/nsmb1038
(23) Oubridge, C.; Ito, N.; Evans, P. R.; Teo, C. H.; Nagai, K. Nature1994, 372, 432. doi: 10.1038/372432a0
(24) Ramos, A.; Grunert, S.; Adams, J.; Micklem, D. R.; Proctor, M.R.; Freund, S.; Bycroft, M.; St Johnston, D.; Varani, G. The EMBO Journal 2000, 19, 997. doi: 10.1093/emboj/19.5.997
(25) Sachs, R.; Max, K. E.; Heinemann, U.; Balbach, J. RNA 2012,18, 65. doi: 10.1261/rna.02809212
(26) Schumacher, M. A.; Pearson, R. F.; Moller, T.; Valentin-Hansen,P.; Brennan, R. G. The EMBO Journal 2002, 21, 3546. doi: 10.1093/emboj/cdf322
(27) Wang, X.; McLachlan, J.; Zamore, P. D.; Hall, T. M. Cell 2002,110, 501. doi: 10.1016/S0092-8674(02)00873-5
(28) Cook, K. B.; Kazan, H.; Zuberi, K.; Morris, Q.; Hughes, T. R.Nucleic Acids Research 2011, 39, D301.
(29) Tian, B.; Bevilacqua, P. C.; Diegelman-Parente, A.; Mathews,M. B. Nature Reviews. Molecular Cell Biology 2004, 5, 1013.doi: 10.1038/nrm1528
(30) Schumacher, M. A.; Karamooz, E.; Zikova, A.; Trantirek, L.;Lukes, J. Cell 2006, 126, 701. doi: 10.1016/j.cell.2006.06.047
(31) Das, R.; Karanicolas, J.; Baker, D. Nature Methods 2010, 7,291. doi: 10.1038/nmeth.1433
(32) Sharma, S.; Ding, F.; Dokholyan, N. V. Bioinformatics 2008, 24,1951. doi: 10.1093/bioinformatics/btn328
(33) Martinez, H. M.; Maizel, J. V., Jr.; Shapiro, B. A. Journal of Biomolecular Structure & Dynamics 2008, 25, 669. doi: 10.1080/07391102.2008.10531240
(34) Parisien, M.; Major, F. Nature 2008, 452, 51. doi: 10.1038/nature06684
(35) Zhao, Y.; Gong, Z.; Xiao, Y. Journal of Biomolecular Structure & Dynamics 2011, 28, 815. doi: 10.1080/07391102.2011.10508609
(36) Shulman-Peleg, A.; Nussinov, R.;Wolfson, H. J. Nucleic Acids Research 2009, 37, D369.
(37) Lewis, B. A.;Walia, R. R.; Terribilini, M.; Ferguson, J.; Zheng,C.; Honavar, V.; Dobbs, D. Nucleic Acids Research 2011, 39,D277.
(38) Wang, Y.; Li, Y.; Ma, Z.; Yang,W.; Ai, C. PLoS Comput. Biol.2010, 6, e1000866.
(39) Jones, S.; Daley, D. T.; Luscombe, N. M.; Berman, H. M.;Thornton, J. M. Nucleic Acids Research 2001, 29, 943. doi: 10.1093/nar/29.4.943
(40) Allers, J.; Shamoo, Y. J. Mol. Biol. 2001, 311, 75. doi: 10.1006/jmbi.2001.4857
(41) Ellis, J. J.; Broom, M.; Jones, S. Proteins 2007, 66, 903.
(42) Chen, Y. C.; Lim, C. Nucleic Acids Research 2008, 36, 7078.doi: 10.1093/nar/gkn868
(43) Bahadur, R. P.; Zacharias, M.; Janin, J. Nucleic Acids Research2008, 36, 2705. doi: 10.1093/nar/gkn102
(44) Shazman, S.; Mandel-Gutfreund, Y. PLoS Comput. Biol. 2008,4, e1000146.
(45) Brandman, R.; Brandman, Y.; Pande, V. S. PLoS One 2012, 7,e30022.
(46) Terribilini, M.; Lee, J. H.; Yan, C.; Jernigan, R. L.; Honavar, V.;Dobbs, D. RNA 2006, 12, 1450. doi: 10.1261/rna.2197306
(47) Kim, O. T.; Yura, K.; Go, N. Nucleic Acids Research 2006, 34,6450. doi: 10.1093/nar/gkl819
(48) Chen, Y. C.; Lim, C. Nucleic Acids Research 2008, 36, e29.
(49) Kumar, M.; Gromiha, M. M.; Raghava, G. P. Proteins 2008, 71,189. doi: 10.1002/prot.v71:1
(50) Zhao, H.; Yang, Y.; Zhou, Y. Nucleic Acids Research 2011, 39,3017.
(51) Perez-Cano, L.; Fernandez-Recio, J. Proteins 2010, 78, 25. doi: 10.1002/prot.22527
(52) Ma, X.; Guo, J.;Wu, J.; Liu, H.; Yu, J.; Xie, J.; Sun, X. Proteins2011, 79, 1230.
(53) Chen, Y.; Kortemme, T.; Robertson, T.; Baker, D.; Varani, G.Nucleic Acids Research 2004, 32, 5147. doi: 10.1093/nar/gkh785
(54) Zheng, S.; Robertson, T. A.; Varani, G. The FEBS Journal 2007,274, 6378. doi: 10.1111/j.1742-4658.2007.06155.x
(55) Perez-Cano, L.; Solernou, A.; Pons, C.; Fernandez-Recio, J.Pac. Symp. Biocomput. 2010, 293.
(56) Katchalski-Katzir, E.; Shariv, I.; Eisenstein, M.; Friesem, A. A.;Aflalo, C.; Vakser, I. A. Proceedings of the National Academy of Sciences of the United States of America 1992, 89, 2195. doi: 10.1073/pnas.89.6.2195
(57) Chen, R.;Weng, Z. Proteins 2002, 47, 281. doi: 10.1002/(ISSN)1097-0134
(58) Gray, J. J.; Moughon, S.;Wang, C.; Schueler-Furman, O.;Kuhlman, B.; Rohl, C. A.; Baker, D. J. Mol. Biol. 2003, 331,281. doi: 10.1016/S0022-2836(03)00670-3
(59) Dominguez, C.; Boelens, R.; Bonvin, A. M. J. Am. Chem. Soc.2003, 125, 1731. doi: 10.1021/ja026939x
(60) Li, L.; Guo, D.; Huang, Y.; Liu, S.; Xiao, Y. BMC Bioinformatics 2011, 12, 36. doi: 10.1186/1471-2105-12-36
(61) Zhang, C.; Lai, L. Journal of Computational Chemistry 2011,32, 2598. doi: 10.1002/jcc.v32.12
(62) Li, C. H.; Cao, L. B.; Su, J. G.; Yang, Y. X.;Wang, C. X.Proteins 2012, 80, 14. doi: 10.1002/prot.v80.1
(63) Setny, P.; Zacharias, M. Nucleic Acids Research 2011, 39, 9118.doi: 10.1093/nar/gkr636
(64) Tuszynska, I.; Bujnicki, J. M. BMC Bioinformatics 2011, 12,348. doi: 10.1186/1471-2105-12-348
(65) Jiang, F.; Kim, S. H. J. Mol. Biol. 1991, 219, 79. doi: 10.1016/0022-2836(91)90859-5
(66) Gabb, H. A.; Jackson, R. M.; Sternberg, M. J. J. Mol. Biol.1997, 272, 106. doi: 10.1006/jmbi.1997.1203
(67) Kozakov, D.; Brenke, R.; Comeau, S. R.; Vajda, S. Proteins2006, 65, 392. doi: 10.1002/prot.21117
(68) Abagyan, R.; Totrov, M. J. Mol. Biol. 1994, 235, 983. doi: 10.1006/jmbi.1994.1052
(69) Wang, C.; Bradley, P.; Baker, D. J. Mol. Biol. 2007, 373, 503.doi: 10.1016/j.jmb.2007.07.050
(70) May, A.; Zacharias, M. Proteins 2008, 70, 794.
(71) Chaudhury, S.; Gray, J. J. J. Mol. Biol. 2008, 381, 1068. doi: 10.1016/j.jmb.2008.05.042
(72) Lesk, V. I.; Sternberg, M. J. Bioinformatics 2008, 24, 1137. doi: 10.1093/bioinformatics/btn093
(73) Smith, G. R.; Sternberg, M. J.; Bates, P. A. J. Mol. Biol. 2005,347, 1077. doi: 10.1016/j.jmb.2005.01.058
(74) Huang, Y.; Liu, Z. J. Mol. Biol. 2009, 393, 1143. doi: 10.1016/j.jmb.2009.09.010
(75) Harel, M.; Spaar, A.; Schreiber, G. Biophys. J. 2009, 96, 4237.doi: 10.1016/j.bpj.2009.02.054
(76) Kim, Y. C.; Tang, C.; Clore, G. M.; Hummer, G. Proceedings of the National Academy of Sciences of the United States of America 2008, 105, 12855. doi: 10.1073/pnas.0802460105
(77) Tang, C.; Iwahara, J.; Clore, G. M. Nature 2006, 444, 383. doi: 10.1038/nature05201
(78) Volkov, A. N.; Ubbink, M.; van Nuland, N. A. J. Biomol. NMR2010, 48, 225. doi: 10.1007/s10858-010-9452-6
(79) Sanchez, I. E.; Ferreiro, D. U.; Dellarole, M.; de Prat-Gay, G.Proceedings of the National Academy of Sciences of the United States of America 2010, 107, 7751. doi: 10.1073/pnas.0911734107
(80) Harel, M.; Cohen, M.; Schreiber, G. J. Mol. Biol. 2007, 371,180. doi: 10.1016/j.jmb.2007.05.032
(81) Fawzi, N. L.; Doucleff, M.; Suh, J. Y.; Clore, G. M.Proceedings of the National Academy of Sciences of the United States of America 2010, 107, 1379. doi: 10.1073/pnas.0909370107
(82) Hwang, H.; Vreven, T.; Janin, J.;Weng, Z. Proteins 2010, 78,3111. doi: 10.1002/prot.v78:15
(83) Liang, S.; Zhang, C.; Liu, S.; Zhou, Y. Nucleic Acids Research2006, 34, 3698. doi: 10.1093/nar/gkl454
(84) Guo, D.; Liu, S. Y.; Huang, Y. Y.; Xiao, Y. Journal of Biomolecular Structure and Dynamics 2012, in press.
(85) Li, X.; Liang, J. Knowledge-Based Energy Functions forComputational Studies of Proteins. In Computational Methods for Protein Structure Prediction and Modeling; Xu, Y., Xu, D.,Liang, J., Eds.; New York: Springer, 2006; Vol. 1; p 71.
(86) Zhou, Y.; Duan, Y.; Yang, Y.; Faraggi, E.; Lei, H. Theoretical Chemistry Accounts 2011, 128, 3. doi: 10.1007/s00214-010-0799-2
(87) Zhou, H.; Skolnick, J. Biophys. J. 2011, 101, 2043. doi: 10.1016/j.bpj.2011.09.012
(88) Czaplewski, C.; Liwo, A.; Makowski, M.; Oldziej, S.;Scheraga, H. A. Coarse-Grained Models of Proteins: Theoryand Applications. In Multiscale Approaches to Protein Modeling; Kolinski, A. Ed.; Springer, 2010; p 35.
(89) Kortemme, T.; Morozov, A. V.; Baker, D. J. Mol. Biol. 2003,326, 1239. doi: 10.1016/S0022-2836(03)00021-4
(90) Jiang, L.; Kuhlman, B.; Kortemme, T.; Baker, D. Proteins2005, 58, 893. doi: 10.1002/prot.20347
(91) Jiang, L.; Lai, L. The Journal of Biological Chemistry 2002,277, 37732. doi: 10.1074/jbc.M204514200
(92) Jiang, L.; Gao, Y.; Mao, F.; Liu, Z.; Lai, L. Proteins 2002, 46,190. doi: 10.1002/(ISSN)1097-0134
(93) Wang, C. X.; Chang, S.; Gong, X. Q.; Yang, F.; Li, C. H.;Chen,W. Z. Acta Phys. -Chim. Sin. 2012, 28, 751. [王存新,常珊, 龚新奇, 杨峰, 李春华, 陈慰祖. 物理化学学报,2012, 28, 751.] doi: 10.3866/PKU.WHXB201202022
(94) Liu, S.; Li, Q.; Lai, L. Proteins 2006, 64, 68. doi: 10.1002/prot.20954
(95) Zacharias, M. Protein Science: a Publication of the Protein Society 2003, 12, 1271.
(96) Liang, S.; Liu, S.; Zhang, C.; Zhou, Y. Proteins 2007, 69, 244.doi: 10.1002/prot.v69:2
(97) Huang, S. Y.; Zou, X. Proteins 2008, 72, 557. doi: 10.1002/prot.21949
(98) Sun,W. T. Advances in Mechanics 2011, 41, 60. [孙卫涛.力学进展, 2011, 41, 60.]
(99) Pierce, B.;Weng, Z. Proteins 2007, 67, 1078. doi: 10.1002/prot.21373
(100) Zhou, H.; Zhou, Y. Protein Science: a Publication of the Protein Society 2002, 11, 2714.
(101) Lu, H.; Skolnick, J. Proteins 2001, 44, 223. doi: 10.1002/(ISSN)1097-0134
(102) Samudrala, R.; Moult, J. J. Mol. Biol. 1998, 275, 895. doi: 10.1006/jmbi.1997.1479
(103) Chuang, G. Y.; Kozakov, D.; Brenke, R.; Comeau, S. R.; Vajda,S. Biophys. J. 2008, 95, 4217. doi: 10.1529/biophysj.108.135814
(104) Liu, S.; Vakser, I. A. BMC Bioinformatics 2011, 12, 280. doi: 10.1186/1471-2105-12-280
(105) Liu, S.; Zhang, C.; Zhou, H.; Zhou, Y. Proteins 2004, 56, 93.doi: 10.1002/prot.20019
(106) Lensink, M. F.; Mendez, R.;Wodak, S. J. Proteins 2007, 69,704. doi: 10.1002/prot.21804
(107) Mendez, R.; Leplae, R.; Lensink, M. F.;Wodak, S. J. Proteins2005, 60, 150. doi: 10.1002/prot.20551
(108) Chang, S.; Jiao, X.; Li, C. H.; Gong, X. Q.; Chen,W. Z.;Wang, C. X. Biophysical Chemistry 2008, 134, 111. doi: 10.1016/j.bpc.2007.12.005
(109) Li, C. H.; Ma, X. H.; Shen, L. Z.; Chang, S.; Chen,W. Z.;Wang, C. X. Biophysical Chemistry 2007, 129, 1. doi: 10.1016/j.bpc.2007.04.014
(110) Guerois, R.; Nielsen, J. E.; Serrano, L. J. Mol. Biol. 2002, 320,369. doi: 10.1016/S0022-2836(02)00442-4
(111) Chen, N. Y.; Su, Z. Y.; Mou, C. Y. Physical Review Letters2006, 96, 078103. doi: 10.1103/PhysRevLett.96.078103
(112) Korkut, A.; Hendrickson,W. A. Proceedings of the National Academy of Sciences of the United States of America 2009,106, 15673. doi: 10.1073/pnas.0907684106
(113) Li,W.;Wolynes, P. G.; Takada, S. Proceedings of the National Academy of Sciences of the United States of America 2011,108, 3504. doi: 10.1073/pnas.1018983108
(114) Ellis, J. J.; Jones, S. Proteins 2008, 70, 1518.
(115) Lindahl, E.; Delarue, M. Nucleic Acids Research 2005, 33,4496. doi: 10.1093/nar/gki730
(116) Cavasotto, C. N.; Kovacs, J. A.; Abagyan, R. A. J. Am. Chem. Soc. 2005, 127, 9632. doi: 10.1021/ja042260c
(117) Petrone, P.; Pande, V. S. Biophys. J. 2006, 90, 1583. doi: 10.1529/biophysj.105.070045
(118) Korkut, A.; Hendrickson,W. A. Proceedings of the National Academy of Sciences of the United States of America 2009,106, 15667. doi: 10.1073/pnas.0907674106
(119) Dobbins, S. E.; Lesk, V. I.; Sternberg, M. J. Proceedings of the National Academy of Sciences of the United States of America2008, 105, 10390. doi: 10.1073/pnas.0802496105
(120) Pons, C.; Solernou, A.; Perez-Cano, L.; Grosdidier, S.;Fernandez-Recio, J. Proteins 2010, 78, 3182. doi: 10.1002/prot.v78:15
(121) Perez-Cano, L.; Jimenez-Garcia, B.; Fernandez-Recio, J.Proteins 2012, 80, 1872.
(122) Barik, A.; Nithin, C.; Manasa, P.; Bahadur, R. P. Proteins 2012,80, 1866.
(123) Hermann, T. Angew Chem. Int. Edit. 2000, 39, 1890. doi: 10.1002/(ISSN)1521-3773
(124) Mackay, J. P.; Font, J.; Segal, D. J. Nature Structural & Molecular Biology 2011, 18, 256. doi: 10.1038/nsmb.2005
(125) Filipovska, A.; Razif, M. F.; Nygard, K. K.; Rackham, O.Nature Chemical Biology 2011, 7, 425. doi: 10.1038/nchembio.577
(126) Dong, S.;Wang, Y.; Cassidy-Amstutz, C.; Lu, G.; Bigler, R.;Jezyk, M. R.; Li, C.; Hall, T. M.;Wang, Z. The Journal of Biological Chemistry 2011, 286, 26732. doi: 10.1074/jbc.M111.244889
(127) Chen, Y.; Varani, G. Chemistry & Biology 2011, 18, 821.
(128) Lu, G.; Dolgner, S. J.; Hall, T. M. Current Opinion in Structural Biology 2009, 19, 110. doi: 10.1016/j.sbi.2008.12.009
(129) Cooke, A.; Prigge, A.; Opperman, L.;Wickens, M.Proceedings of the National Academy of Sciences of the United States of America 2011, 108, 15870. doi: 10.1073/pnas.1105151108
(130) Koh, Y. Y.;Wang, Y.; Qiu, C.; Opperman, L.; Gross, L.; TanakaHall, T. M.;Wickens, M. RNA 2011, 17, 718. doi: 10.1261/rna.2540311
(131) Wells, J. A.; McClendon, C. L. Nature 2007, 450, 1001. doi: 10.1038/nature06526
(132) Arkin, M. R.;Wells, J. A. Nat. Rev. Drug. Discov. 2004, 3, 301.doi: 10.1038/nrd1343
(133) Arkin, M. Curr. Opin. Chem. Biol. 2005, 9, 317. doi: 10.1016/j.cbpa.2005.03.001
(134) Bourgeas, R.; Basse, M. J.; Morelli, X.; Roche, P. PloS One2010, 5, e9598.
(135) Zhang, C.; Lai, L. Biochemical Society Transactions 2011, 39,1382. doi: 10.1042/BST0391382
(136) Liu, S.; Zhu, X.; Liang, H.; Cao, A.; Chang, Z.; Lai, L.Proceedings of the National Academy of Sciences of the United States of America 2007, 104, 5330. doi: 10.1073/pnas.0606198104
(137) Fleishman, S. J.; Whitehead, T. A.; Ekiert, D. C.; Dreyfus, C.;Corn, J. E.; Strauch, E. M.;Wilson, I. A.; Baker, D. Science2011, 332, 816. doi: 10.1126/science.1202617
(138) Der, B. S.; Kuhlman, B. Science 2011, 332, 801. doi: 10.1126/science.1207082
(139) Zhang, C.; Lai, L. Proteins 2012, 80, 1078. doi: 10.1002/prot.v80.4
(140) Bai, H. J.; Lai, L. H. Acta Phys. -Chim. Sin. 2010, 26, 1988.[白红军, 来鲁华. 物理化学学报, 2010, 26, 1988.] doi: 10.3866/PKU.WHXB20100725

[1]	Ying-Chun DENG,Qing LIU,Qiang HUANG. Molecular Docking of Human-Like Receptor to Hemagglutinins of Avian Influenza A Viruses [J]. Acta Phys. -Chim. Sin., 2017, 33(3): 633-641.
[2]	Yu-Ling DENG,Lu YU,Qiang HUANG. A Multi-Target Docking System of Human Kinome [J]. Acta Phys. -Chim. Sin., 2016, 32(9): 2355-2363.
[3]	Shi-Wen XU,Dong-Qiang LIN,Shan-Jing YAO. Evaluation of Molecular Binding Modes on Site Ⅱ of Human Serum Albumin [J]. Acta Phys. -Chim. Sin., 2016, 32(7): 1819-1828.
[4]	Feng LIN,Xin-Mei FU,Chao WANG,Si-Yu JIANG,Jing-Hui WANG,Shu-Wei ZHANG,Ling YANG,Yan LI. QSAR, Molecular Docking and Molecular Dynamics of 3C-like Protease Inhibitors [J]. Acta Phys. -Chim. Sin., 2016, 32(11): 2693-2708.
[5]	Qi-Yao LUO,Zi-Yun WANG,Hong-Wei JIN,Zhen-Ming LIU,Liang-Ren ZHANG. Improved Docking-Based Virtual Screening Using the Score Correction Strategy for Specific Endothelial Lipase Inhibitors Identification [J]. Acta Phys. -Chim. Sin., 2016, 32(10): 2606-2619.
[6]	Shu-Zhen. ZHANG,Chao. ZHENG,Chang-Jin. ZHU. Molecular Docking and Receptor-Based 3D-QSAR Studies on Aromatic Thiazine Derivatives as Selective Aldose Reductase Inhibitors [J]. Acta Phys. -Chim. Sin., 2015, 31(12): 2395-2404.
[7]	Hai-Chun. LIU,Shuai. LU,Ting. RAN,Yan-Min. ZHANG,Jin-Xing. XU,Xiao. XIONG,An-Yang. XU,Tao. LU,Ya-Dong. CHEN. 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.
[8]	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.
[9]	BAI Shu, ZHOU Rong, LIU Fu-Feng. Rational Design of Affinity Ligand for the Oriented Immobilization of Trypsin [J]. Acta Phys. -Chim. Sin., 2013, 29(02): 439-448.
[10]	QIAO Kang, ZENG Ling-Xiao, JIN Hong-Wei, LIU Zhen-Ming, ZHANG Liang-Ren. QSAR Analysis of Human Adenosine A₃ Receptor Antagonists [J]. Acta Phys. -Chim. Sin., 2012, 28(06): 1509-1519.
[11]	SHEN Tao, DU Feng-Pei, LIU Ting, YAO Guang-Wei, WU Zheng, FANG Meng-Meng, XU Xiao-Jie, LU Hui-Zhe. Molecular Simulation of the Interaction between Imidazole Glycerol Phosphate Dehydrase and Nitrogen-Containing Heterocyclic Phosphate Inhibitors [J]. Acta Phys. -Chim. Sin., 2011, 27(08): 1831-1838.
[12]	ZHANG Yuan, CHEN Ya-Dong, YOU Qi-Dong, ZOU Li-Yun, YANG Yan. Homology Modeling and Molecular Docking Studies on the Selectivity of HDAC1/HDAC8 [J]. Acta Phys. -Chim. Sin., 2010, 26(06): 1676-1686.
[13]	ZHENG Chun-Song, XU Xiao-Jie, LIU Xian-Xiang, YE Hong-Zhi. Computational Pharmacology of Jingzhi Tougu Xiaotong Granule in Preventing and Treating Osteoarthritis [J]. Acta Phys. -Chim. Sin., 2010, 26(03): 775-783.
[14]	LI Bo, LIU Ming, HU Wen-Xiang. Molecular Docking and Molecular Dynamics Simulations of Fentanyl Analogs Binding to μ-Opioid Receptors [J]. Acta Phys. -Chim. Sin., 2010, 26(01): 206-214.
[15]	LIU Tao, SUN Mao-Tang, DONG Xiao-Wu, REN Xin, YANG Xin, DU Li-Lin, HU Yong-Zhou. Structure-Based Drug Design, Synthesis and Antitumor Activities of Novel CDK7 Inhibitors [J]. Acta Phys. -Chim. Sin., 2009, 25(10): 2107-2112.

Protein-RNA Interaction Interface Prediction and Design

PDF (PC)

Like

Knowledge

Abstract

Cite this article

share this article

References

Related Articles 15

Metrics

Comments

Recommended 0