Chinese Physics B, Volume. 29, Issue 10, (2020)
Review of multimer protein–protein interaction complex topology and structure prediction
[1] J Janin. Molecular bioSystems, 6, 2351(2010).
[2] G Sudha, R Nussinov, N Srinivasan. Prog. Biophys. Mol. Biol., 116, 141(2014).
[3] T M Zhou, S Wang, J Xu. bioRxiv(2018).
[4] H Zeng, S Wang, T Zhou, F Zhao, X Li, Q Wu, J Xu. Nucleic Acids Research, 46, W432(2018).
[5] T Ching, D S Himmelstein, B K Beaulieu-Jones et al. J. R. Soc. Interface, 15(2018).
[6] S Wang, S Sun, Z Li, R Zhang, J Xu. PLoS Comput. Biol., 13(2017).
[7] S Wang, W Li, S Liu, J Xu. Nucleic Acids Research, 44, W430(2016).
[8] H Kamisetty, S Ovchinnikov, D Baker. Proc. Natl. Acad. Sci. USA, 110(2013).
[9] S Balakrishnan, H Kamisetty, J G Carbonell, S I Lee, C J Langmead. Proteins, 79, 1061(2011).
[10] S Ovchinnikov, H Kamisetty, D Baker. Elife, 3(2014).
[11] B Adhikari, J Hou, J Cheng. Bioinformatics, 34, 1466(2018).
[12] D T Jones, D W Buchan, D Cozzetto, M Pontil. Bioinformatics, 28, 184(2012).
[13] L Kaján, T A Hopf, M Kalaš, D S Marks, B Rost. BMC Bioinformatics, 15, 85(2014).
[14] S Wang, W Li, R Zhang, S Liu, J Xu. Nucleic Acids Res., 44, W361(2016).
[15] G Xu, Q Wang, J Ma. Journal of Chemical Theory and Computation, 16, 3970(2020).
[16] Z Zhao, X Gong. IEEEACM Transactions on Computational Biology and Bioinformatics, 16, 1753(2019).
[17] D Sun, X Gong. Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics(2020).
[18] J Liu, X Gong. BMC Bioinformatics, 20, 609(2019).
[19] T Vreven, H Hwang, B G Pierce, Z Weng. Brief Bioinform, 15, 169(2014).
[20] Q Zhang, T Feng, L Xu, H Sun, P Pan, Y Li, D Li, T Hou. Curr. Drug Targets, 17, 1586(2016).
[21] D W Ritchie, G J Kemp. Proteins: Structure, Function, and Bioinformatics, 39, 178(2000).
[22] K Lee, C Czaplewski, S Y Kim, J Lee. Journal of Computational Chemistry, 26, 78(2005).
[23] D W Ritchie. Proteins: Structure, Function, and Bioinformatics, 52, 98(2003).
[24] B Pierce, W Tong, Z Weng. Bioinformatics, 21, 1472(2005).
[25] R Chen, L Li, Z Weng. Proteins, 52, 80(2003).
[26] I André, P Bradley, C Wang, D Baker. Proc. Natl. Acad. Sci. USA, 104(2007).
[27] S R Comeau, D W Gatchell, S Vajda, C J Camacho. Bioinformatics, 20, 45(2004).
[28] Y Yan, H Tao, J He, S Y Huang. Nature Protocols, 15, 1829(2020).
[29] Y Yan, D Zhang, P Zhou, B Li, S Y Huang. Nucleic Acids Res., 45, W365(2017).
[30] Y Yan, H Tao, S Y Huang. Nucleic Acids Res., 46, W423(2018).
[31] D W Ritchie, S Grudinin. Journal of Applied Crystallography, 49, 158(2016).
[32] H Yu, N M Luscombe, H X Lu, X Zhu, Y Xia, J D J Han, N Bertin, S Chung, M Vidal, M Gerstein. Genome Research, 14, 1107(2004).
[33] P Aloy, R B Russell. Proc. Natl. Acad. Sci. USA, 99, 5896(2002).
[34] P Aloy, R B Russell. Bioinformatics, 19, 161(2003).
[35] L Lu, H Lu, J Skolnick. Proteins, 49, 350(2002).
[36] H Chen, J Skolnick. Biophys J., 94, 918(2008).
[37] G Launay, T Simonson. BMC Bioinformatics, 9, 427(2008).
[38] P Aloy, B Böttcher, H Ceulemans, C Leutwein, C Mellwig, S Fischer, A C Gavin, P Bork, G Superti-Furga, L Serrano. Science, 303, 2026(2004).
[39] T M W Nye, C Berzuini, W R Gilks, M M Babu, S A Teichmann. Bioinformatics, 21, 993(2004).
[40] E Krissinel, K Henrick. Journal of Molecular Biology, 372, 774(2007).
[41] Q Xu, R L Dunbrack. Nucleic Acids Res., 39, D761(2010).
[42] H Yu, P Braun, M A Yildirim, I Lemmens, K Venkatesan, J Sahalie, T Hirozane-Kishikawa, F Gebreab, N Li, N Simonis, T Hao, J F Rual, A Dricot, A Vazquez, R R Murray, C Simon, L Tardivo, S Tam, N Svrzikapa, C Fan, A S de Smet, A Motyl, M E Hudson, J Park, X Xin, M E Cusick, T Moore, C Boone, M Snyder, F P Roth, A L Barabási, J Tavernier, D E Hill, M Vidal. Science, 322, 104(2008).
[43] K Tarassov, V Messier, C R Landry, S Radinovic, M M Serna Molina, I Shames, Y Malitskaya, J Vogel, H Bussey, S W Michnick. Science, 320, 1465(2008).
[44] N J Krogan, G Cagney, H Yu et al. Nature, 440, 637(2006).
[45] A C Gavin, P Aloy, P Grandi, R Krause, M Boesche, M Marzioch, C Rau, L J Jensen, S Bastuck, B Dümpelfeld, A Edelmann, M A Heurtier, V Hoffman, C Hoefert, K Klein, M Hudak, A M Michon, M Schelder, M Schirle, M Remor, T Rudi, S Hooper, A Bauer, T Bouwmeester, G Casari, G Drewes, G Neubauer, J M Rick, B Kuster, P Bork, R B Russell, G Superti-Furga. Nature, 440, 631(2006).
[46] N Pržulj. Bioessays, 33, 115(2011).
[47] H Yu, P M Kim, E Sprecher, V Trifonov, M Gerstein. PLoS Comput. Biol., 3, e59(2007).
[48] H Jeong, S P Mason, A L Barabási, Z N Oltvai. Nature, 411, 41(2001).
[49] J D J Han, N Bertin, T Hao, D S Goldberg, G F Berriz, L V Zhang, D Dupuy, A J M Walhout, M E Cusick, F P Roth, M Vidal. Nature, 430, 88(2004).
[50] J Wang, M Li, Y Deng, Y Pan. BMC Genomics, 11, S10(2010).
[51] I Ulitsky, R Shamir. Bioinformatics, 25, 1158(2009).
[52] R Sharan, I Ulitsky, R Shamir. Mol. Syst. Biol., 3, 88(2007).
[53] K Lee, H Y Chuang, A Beyer, M K Sung, W K Huh, B Lee, T Ideker. Nucleic Acids Res., 36, e136(2008).
[54] A D King, N Przulj, I Jurisica. Bioinformatics, 20, 3013(2004).
[55] C C Friedel, J Krumsiek, R Zimmer. J. Comput. Biol., 16, 971(2009).
[56] H N Chua, W K Sung, L Wong. Bioinformatics, 22, 1623(2006).
[57] G D Bader, C W V Hogue. Nature Biotechnology, 20, 991(2002).
[58] S Asthana, O D King, F D Gibbons, F P Roth. Genome Research, 14, 1170(2004).
[59] Y A Kim, S Wuchty, T M Przytycka. PLoS Comput. Biol., 7(2011).
[60] T Ideker, R Sharan. Genome Research, 18, 644(2008).
[61] C A Hidalgo, N Blumm, A L Barabási, N A Christakis. PLoS Comput. Biol., 5(2009).
[62] G Hannum, R Srivas, A Guénolé, H van Attikum, N J Krogan, R M Karp, T Ideker. PLoS Genet., 5(2009).
[63] H Y Chuang, E Lee, Y T Liu, D Lee, T Ideker. Molecular Systems Biology, 3, 140(2007).
[64] H Huang, B M Jedynak, J S Bader. PLoS Comput. Biol., 3, e214(2007).
[65] C Lei, J Ruan. 2012 IEEE International Conference on Bioinformatics and Biomedicine, 1-6.
[66] S Srihari, C H Yong, L Wong. Computational prediction of protein complexes from protein interaction networks(2017).
[67] G D Bader, C W Hogue. BMC bioinformatics, 4, 2(2003).
[68] J B Pereira Leal, A J Enright, C A Ouzounis. PROTEINS: Structure, Function, and Bioinformatics, 54, 49(2004).
[69] S Brohee, J Van Helden. BMC Bioinformatics, 7, 488(2006).
[70] S Pu, J Vlasblom, A Emili, J Greenblatt, S J Wodak. Proteomics, 7, 944(2007).
[71] M Blatt, S Wiseman, E Domany. Phys. Rev. Lett., 76, 3251(1996).
[72] G Getz, M Vendruscolo, D Sachs, E Domany. Proteins: Structure, Function, and Bioinformatics, 46, 405(2002).
[73] G Getz, E Levine, E Domany. Proc. Natl. Acad. Sci. USA, 97(2000).
[74] V Spirin, L A Mirny. Proc. Natl. Acad. Sci. USA, 100(2003).
[75] X L Li, C S Foo, S H Tan, S K Ng. Genome Informatics, 16, 260(2005).
[76] Y Qi, F Balem, C Faloutsos, J Klein-Seetharaman, Z Bar-Joseph. Bioinformatics, 24, i250(2008).
[77] C H Yong, G Liu, H N Chua, L Wong. BMC Systems Biology, S13.
[78] S Srihari, H W Leong. International Journal of Bioinformatics Research and Applications, 8, 286(2012).
[79] B Adamcsek, G Palla, I J Farkas, I Derenyi, T Vicsek. Bioinformatics, 22, 1021(2006).
[80] M Altaf-Ul-Amin, Y Shinbo, K Mihara, K Kurokawa, S Kanaya. BMC Bioinformatics, 7, 207(2006).
[81] M Li, J E Chen, J X Wang, B Hu, G Chen. BMC Bioinformatics, 9, 398(2008).
[82] G Liu, L Wong, H N Chua. Bioinformatics, 25, 1891(2009).
[83] T Nepusz, H Yu, A Paccanaro. Nat. Methods, 9, 471(2012).
[84] H Wang, B Kakaradov, S R Collins, L Karotki, D Fiedler, M Shales, K M Shokat, T C Walther, N J Krogan, D Koller. Mol. Cell Proteomics, 8, 1361(2009).
[85] H Tong, C Faloutsos, J Y Pan. Sixth international conference on data mining (ICDM’06), 613-622.
[86] F Radicchi, C Castellano, F Cecconi, V Loreto, D Parisi. Proc. Natl. Acad. Sci. USA, 101, 2658(2004).
[87] A Li, S Horvath. Bioinformatics, 23, 222(2007).
[88] F Fouss, A Pirotte, J Renders, M Saerens. IEEE Transactions on Knowledge and Data Engineering, 19, 355(2007).
[89] L Lü, T Zhou. Physica A, 390, 1150(2011).
[90] C Wang, C Ding, Q Yang, S R Holbrook. Genome Biol., 8, R271(2007).
[91] Y Fang, W Benjamin, M Sun, K Ramani. PLoS One, 6(2011).
[92] Q Xu, E W Xiang, Q Yang. Proteomics, 11, 3818(2011).
[93] Y Park, J S Bader. BMC Bioinformatics, 12, S44(2011).
[94] O Kuchaiev, M Rasajski, D J Higham, N Przulj. PLoS Comput. Biol., 5(2009).
[95] C Lei, J Ruan. Bioinformatics, 29, 355(2012).
[96] L Wang, K Hu, Y Tang. Current Bioinformatics, 9, 246(2014).
[97] L Bartoli, E Capriotti, P Fariselli, P L Martelli, R Casadio. Methods Mol. Biol., 413, 199(2008).
[98] M Vassura, L Margara, P Di Lena, F Medri, P Fariselli, R Casadio. IEEEACM Trans. Comput. Biol. Bioinform., 5, 357(2008).
[99] M Vendruscolo, E Kussell, E Domany. Fold Des., 2, 295(1997).
[100] H Breu, D G Kirkpatrick. Computational Geometry, 9, 3(1998).
[101] C Zhang, S M Mortuza, B He, Y Wang, Y Zhang. Proteins, 86, 136(2018).
[102] D Baú, A J M Martin, C Mooney, A Vullo, I Walsh, G Pollastri. BMC Bioinformatics, 7, 402(2006).
[103] P Kukic, C Mirabello, G Tradigo, I Walsh, P Veltri, G Pollastri. BMC Bioinformatics, 15, 6(2014).
[104] I Walsh, D Baù, A J M Martin, C Mooney, A Vullo, G Pollastri. BMC Structural Biology, 9, 5(2009).
[105] P Fariselli, R Casadio. Bioinformatics, 17, 957(2001).
[106] P L Martelli, P Fariselli, L Malaguti, R Casadio. Protein Engineering, Design and Selection, 15, 951(2002).
[107] A Ceroni, A Passerini, A Vullo, P Frasconi. Nucleic Acids Res., 34, W177(2006).
[108] C H Tsai, B J Chen, C H Chan, H L Liu, C Y Kao. Bioinformatics, 21, 4416(2005).
[109] A Vullo, P Frasconi. Bioinformatics, 20, 653(2004).
[110] F Ferrè, P Clote. Nucleic Acids Res, 33, W230(2005).
[111] J Schaarschmidt, B Monastyrskyy, A Kryshtafovych, A Bonvin. Proteins, 86, 51(2018).
[112] S Seemayer, M Gruber, J Söding. Bioinformatics, 30, 3128(2014).
[113] D T Jones, S M Kandathil. Bioinformatics, 34, 3308(2018).
[114] J Hanson, K Paliwal, T Litfin, Y Yang, Y Zhou. Bioinformatics, 34, 4039(2018).
[115] A W Senior, R Evans, J Jumper, J Kirkpatrick, L Sifre, T Green, C Qin, A Žídek, A W Nelson, A Bridgland. Proteins: Structure, Function, and Bioinformatics, 87, 1141(2019).
[116] Q Dong, X Wang, L Lin, Y Guan. BMC Bioinformatics, 8, 147(2007).
[117] F u A A Minhas, B J Geiss, A Ben-Hur. Proteins, 82, 1142(2014).
[118] H Zellner, M Staudigel, T Trenner, M Bittkowski, V Wolowski, C Icking, R Merkl. Proteins, 80, 154(2012).
[119] B Wang, P Chen, D S Huang, J J Li, T M Lok, M R Lyu. FEBS Lett., 580, 380(2006).
[120] J R Bradford, D R Westhead. Bioinformatics, 21, 1487(2005).
[121] A Koike, T Takagi. Protein Eng. Des. Sel., 17, 165(2004).
[122] B K Sriwastava, S Basu, U Maulik. J. Biosci., 40, 809(2015).
[123] G Singh, K Dhole, P P Pai, S Mondal. SPRINGS: prediction of protein–protein interaction sites using artificial neural networks(2014).
[124] Y Ofran, B Rost. Bioinformatics, 23, e13(2007).
[125] H Chen, H X Zhou. Proteins, 61, 21(2005).
[126] Y Ofran, B Rost. FEBS Lett., 544, 236(2003).
[127] P Fariselli, F Pazos, A Valencia, R Casadio. Eur. J. Biochem., 269, 1356(2002).
[128] H X Zhou, Y Shan. Proteins: Structure, Function, and Bioinformatics, 44, 336(2001).
[129] J R Bradford, C J Needham, A J Bulpitt, D R Westhead. J. Mol. Biol., 362, 365(2006).
[130] H Neuvirth, R Raz, G Schreiber. J. Mol. Biol., 338, 181(2004).
[131] H Geng, T Lu, X Lin, Y Liu, F Yan. Biochemistry Research International, 2015(2015).
[132] Y Murakami, K Mizuguchi. Bioinformatics, 26, 1841(2010).
[133] X W Chen, J C Jeong. Bioinformatics, 25, 585(2009).
[134] T C Northey, A Barešić, A C R Martin. Bioinformatics, 34, 223(2018).
[135] B Q Li, K Y Feng, L Chen, T Huang, Y D Cai. PLoS One, 7(2012).
[136] M Sikić, S Tomić, K Vlahovicek. PLoS Comput. Biol., 5(2009).
[137] Z S Wei, J Y Yang, H B Shen, D J Yu. IEEE Trans. Nanobioscience, 14, 746(2015).
[138] M H Li, L Lin, X L Wang, T Liu. Bioinformatics, 23, 597(2007).
[139] D D Wang, R Wang, H Yan. Neurocomputing, 128, 258(2014).
[140] K Dhole, G Singh, P P Pai, S Mondal. J. Theor. Biol., 348, 47(2014).
[141] J Jia, Z Liu, X Xiao, B Liu, K C Chou. J. Biomol. Struct. Dyn., 34, 1946(2016).
[142] L Deng, J Guan, Q Dong, S Zhou. BMC Bioinformatics, 10, 426(2009).
[143] P Chen, J Li. BMC Bioinformatics, 11, 402(2010).
[144] X Du, S Sun, C Hu, X Li, J Xia. J. Biol. Res. (Thessalon), 23, 10(2016).
[145] A Krizhevsky, I Sutskever, G E Hinton. Advances in Neural Information Processing Systems, 1097-1105.
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Daiwen Sun, Shijie Liu, Xinqi Gong. Review of multimer protein–protein interaction complex topology and structure prediction[J]. Chinese Physics B, 2020, 29(10):
Received: Jun. 29, 2020
Accepted: --
Published Online: Apr. 21, 2021
The Author Email: Gong Xinqi (xinqigong@ruc.edu.cn)