Decoding Protein-protein Interactions: An Overview

Olivia       Slater; Bethany       Miller; Maria       Kontoyianni
Abstract

Drug discovery has focused on the paradigm “one drug, one target” for a long time. However, small molecules can act at multiple macromolecular targets, which serves as the basis for drug repurposing. In an effort to expand the target space, and given advances in X-ray crystallography, protein-protein interactions have become an emerging focus area of drug discovery enterprises. Proteins interact with other biomolecules and it is this intricate network of interactions that determines the behavior of the system and its biological processes. In this review, we briefly discuss networks in disease, followed by computational methods for protein-protein complex prediction. Computational methodologies and techniques employed towards objectives such as protein-protein docking, protein-protein interactions, and interface predictions are described extensively. Docking aims at producing a complex between proteins, while interface predictions identify a subset of residues on one protein that could interact with a partner, and protein-protein interaction sites address whether two proteins interact. In addition, approaches to predict hot spots and binding sites are presented along with a representative example of our internal project on the chemokine CXC receptor 3 B-isoform and predictive modeling with IP10 and PF4.
Keywords: Protein-protein interactions, protein-protein interface, disease networks, hot spots, molecular recognition, proteinprotein docking, machine learning methods, binding site identification.
Graphical Abstract

[1] 
Vidal, M.; Cusick, M.E.; Barabási, A.L. Interactome networks and human disease. Cell,  2011, 144(6), 986-998.
[http://dx.doi.org/10.1016/j.cell.2011.02.016] [PMID: 21414488] 
[2] 
Kim, M.S.; Pinto, S.M.; Getnet, D.; Nirujogi, R.S.; Manda, S.S.; Chaerkady, R.; Madugundu, A.K.; Kelkar, D.S.; Isserlin, R.; Jain, S.; Thomas, J.K.; Muthusamy, B.; Leal-Rojas, P.; Kumar, P.; Sahasrabuddhe, N.A.; Balakrishnan, L.; Advani, J.; George, B.; Renuse, S.; Selvan, L.D.; Patil, A.H.; Nanjappa, V.; Radhakrishnan, A.; Prasad, S.; Subbannayya, T.; Raju, R.; Kumar, M.; Sreenivasamurthy, S.K.; Marimuthu, A.; Sathe, G.J.; Chavan, S.; Datta, K.K.; Subbannayya, Y.; Sahu, A.; Yelamanchi, S.D.; Jayaram, S.; Rajagopalan, P.; Sharma, J.; Murthy, K.R.; Syed, N.; Goel, R.; Khan, A.A.; Ahmad, S.; Dey, G.; Mudgal, K.; Chatterjee, A.; Huang, T.C.; Zhong, J.; Wu, X.; Shaw, P.G.; Freed, D.; Zahari, M.S.; Mukherjee, K.K.; Shankar, S.; Mahadevan, A.; Lam, H.; Mitchell, C.J.; Shankar, S.K.; Satishchandra, P.; Schroeder, J.T.; Sirdeshmukh, R.; Maitra, A.; Leach, S.D.; Drake, C.G.; Halushka, M.K.; Prasad, T.S.; Hruban, R.H.; Kerr, C.L.; Bader, G.D.; Iacobuzio-Donahue, C.A.; Gowda, H.; Pandey, A. A draft map of the human proteome. Nature,  2014, 509(7502), 575-581.
[http://dx.doi.org/10.1038/nature13302] [PMID: 24870542] 
[3] 
Wilhelm, M.; Schlegl, J.; Hahne, H.; Gholami, A.M.; Lieberenz, M.; Savitski, M.M.; Ziegler, E.; Butzmann, L.; Gessulat, S.; Marx, H.; Mathieson, T.; Lemeer, S.; Schnatbaum, K.; Reimer, U.; Wenschuh, H.; Mollenhauer, M.; Slotta-Huspenina, J.; Boese, J.H.; Bantscheff, M.; Gerstmair, A.; Faerber, F.; Kuster, B. Mass-spectrometry-based draft of the human proteome. Nature,  2014, 509(7502), 582-587.
[http://dx.doi.org/10.1038/nature13319] [PMID: 24870543] 
[4] 
Rolland, T.; Taşan, M.; Charloteaux, B.; Pevzner, S.J.; Zhong, Q.; Sahni, N.; Yi, S.; Lemmens, I.; Fontanillo, C.; Mosca, R.; Kamburov, A.; Ghiassian, S.D.; Yang, X.; Ghamsari, L.; Balcha, D.; Begg, B.E.; Braun, P.; Brehme, M.; Broly, M.P.; Carvunis, A.R.; Convery-Zupan, D.; Corominas, R.; Coulombe-Huntington, J.; Dann, E.; Dreze, M.; Dricot, A.; Fan, C.; Franzosa, E.; Gebreab, F.; Gutierrez, B.J.; Hardy, M.F.; Jin, M.; Kang, S.; Kiros, R.; Lin, G.N.; Luck, K.; MacWilliams, A.; Menche, J.; Murray, R.R.; Palagi, A.; Poulin, M.M.; Rambout, X.; Rasla, J.; Reichert, P.; Romero, V.; Ruyssinck, E.; Sahalie, J.M.; Scholz, A.; Shah, A.A.; Sharma, A.; Shen, Y.; Spirohn, K.; Tam, S.; Tejeda, A.O.; Trigg, S.A.; Twizere, J.C.; Vega, K.; Walsh, J.; Cusick, M.E.; Xia, Y.; Barabási, A.L.; Iakoucheva, L.M.; Aloy, P.; De Las Rivas, J.; Tavernier, J.; Calderwood, M.A.; Hill, D.E.; Hao, T.; Roth, F.P.; Vidal, M. A proteome-scale map of the human interactome network. Cell,  2014, 159(5), 1212-1226.
[http://dx.doi.org/10.1016/j.cell.2014.10.050] [PMID: 25416956] 
[5] 
Barabási, A.L.; Gulbahce, N.; Loscalzo, J. Network medicine: a network-based approach to human disease. Nat. Rev. Genet.,  2011, 12(1), 56-68.
[http://dx.doi.org/10.1038/nrg2918] [PMID: 21164525] 
[6] 
Zhao, Y.; Jensen, O.N. Modification-specific proteomics: strategies for characterization of post-translational modifications using enrichment techniques. Proteomics,  2009, 9(20), 4632-4641.
[http://dx.doi.org/10.1002/pmic.200900398] [PMID: 19743430] 
[7] 
Venkatesan, K.; Rual, J.F.; Vazquez, A.; Stelzl, U.; Lemmens, I.; Hirozane-Kishikawa, T.; Hao, T.; Zenkner, M.; Xin, X.; Goh, K.I.; Yildirim, M.A.; Simonis, N.; Heinzmann, K.; Gebreab, F.; Sahalie, J.M.; Cevik, S.; Simon, C.; de Smet, A.S.; Dann, E.; Smolyar, A.; Vinayagam, A.; Yu, H.; Szeto, D.; Borick, H.; Dricot, A.; Klitgord, N.; Murray, R.R.; Lin, C.; Lalowski, M.; Timm, J.; Rau, K.; Boone, C.; Braun, P.; Cusick, M.E.; Roth, F.P.; Hill, D.E.; Tavernier, J.; Wanker, E.E.; Barabási, A.L.; Vidal, M. An empirical framework for binary interactome mapping. Nat. Methods,  2009, 6(1), 83-90.
[http://dx.doi.org/10.1038/nmeth.1280] [PMID: 19060904] 
[8] 
Goldstein, D.B. Common genetic variation and human traits. N. Engl. J. Med.,  2009, 360(17), 1696-1698.
[http://dx.doi.org/10.1056/NEJMp0806284] [PMID: 19369660] 
[9] 
Schadt, E.E. Molecular networks as sensors and drivers of common human diseases. Nature,  2009, 461(7261), 218-223.
[http://dx.doi.org/10.1038/nature08454] [PMID: 19741703] 
[10] 
Visscher, P.M.; Hill, W.G.; Wray, N.R. Heritability in the genomics era--concepts and misconceptions. Nat. Rev. Genet.,  2008, 9(4), 255-266.
[http://dx.doi.org/10.1038/nrg2322] [PMID: 18319743] 
[11] 
Witte, JS Genome-wide association studies and beyond. Annu Rev
  Public Health,  2010, 31(9-20 24), 20.
[http://dx.doi.org/10.1146/annurev.publhealth.012809.103723] 
[12] 
Goh, K.I.; Cusick, M.E.; Valle, D.; Childs, B.; Vidal, M.; Barabási, A.L. The human disease network. Proc. Natl. Acad. Sci. USA,  2007, 104(21), 8685-8690.
[http://dx.doi.org/10.1073/pnas.0701361104] [PMID: 17502601] 
[13] 
Trujillano, D.; Oprea, G.E.; Schmitz, Y.; Bertoli-Avella, A.M.; Abou Jamra, R.; Rolfs, A. A comprehensive global genotype-phenotype database for rare diseases. Mol. Genet. Genomic Med.,  2016, 5(1), 66-75.
[http://dx.doi.org/10.1002/mgg3.262] [PMID: 28116331] 
[14] 
Rual, J.F.; Venkatesan, K.; Hao, T.; Hirozane-Kishikawa, T.; Dricot, A.; Li, N.; Berriz, G.F.; Gibbons, F.D.; Dreze, M.; Ayivi-Guedehoussou, N.; Klitgord, N.; Simon, C.; Boxem, M.; Milstein, S.; Rosenberg, J.; Goldberg, D.S.; Zhang, L.V.; Wong, S.L.; Franklin, G.; Li, S.; Albala, J.S.; Lim, J.; Fraughton, C.; Llamosas, E.; Cevik, S.; Bex, C.; Lamesch, P.; Sikorski, R.S.; Vandenhaute, J.; Zoghbi, H.Y.; Smolyar, A.; Bosak, S.; Sequerra, R.; Doucette-Stamm, L.; Cusick, M.E.; Hill, D.E.; Roth, F.P.; Vidal, M. Towards a proteome-scale map of the human protein-protein interaction network. Nature,  2005, 437(7062), 1173-1178.
[http://dx.doi.org/10.1038/nature04209] [PMID: 16189514] 
[15] 
Stelzl, U.; Worm, U.; Lalowski, M.; Haenig, C.; Brembeck, F.H.; Goehler, H.; Stroedicke, M.; Zenkner, M.; Schoenherr, A.; Koeppen, S.; Timm, J.; Mintzlaff, S.; Abraham, C.; Bock, N.; Kietzmann, S.; Goedde, A.; Toksöz, E.; Droege, A.; Krobitsch, S.; Korn, B.; Birchmeier, W.; Lehrach, H.; Wanker, E.E. A human protein-protein interaction network: a resource for annotating the proteome. Cell,  2005, 122(6), 957-968.
[http://dx.doi.org/10.1016/j.cell.2005.08.029] [PMID: 16169070] 
[16] 
Skinnider, M.A.; Stacey, R.G.; Foster, L.J. Genomic data integration systematically biases interactome mapping. PLOS Comput. Biol.,  2018, 14(10), e1006474
[http://dx.doi.org/10.1371/journal.pcbi.1006474] [PMID: 30332399] 
[17] 
Huttlin, E.L.; Ting, L.; Bruckner, R.J.; Gebreab, F.; Gygi, M.P.; Szpyt, J.; Tam, S.; Zarraga, G.; Colby, G.; Baltier, K.; Dong, R.; Guarani, V.; Vaites, L.P.; Ordureau, A.; Rad, R.; Erickson, B.K.; Wühr, M.; Chick, J.; Zhai, B.; Kolippakkam, D.; Mintseris, J.; Obar, R.A.; Harris, T.; Artavanis-Tsakonas, S.; Sowa, M.E.; De Camilli, P.; Paulo, J.A.; Harper, J.W.; Gygi, S.P. The bioplex network: A systematic exploration of the human interactome. Cell,  2015, 162(2), 425-440.
[http://dx.doi.org/10.1016/j.cell.2015.06.043] [PMID: 26186194] 
[18] 
Huttlin, E.L.; Bruckner, R.J.; Paulo, J.A.; Cannon, J.R.; Ting, L.; Baltier, K.; Colby, G.; Gebreab, F.; Gygi, M.P.; Parzen, H.; Szpyt, J.; Tam, S.; Zarraga, G.; Pontano-Vaites, L.; Swarup, S.; White, A.E.; Schweppe, D.K.; Rad, R.; Erickson, B.K.; Obar, R.A.; Guruharsha, K.G.; Li, K.; Artavanis-Tsakonas, S.; Gygi, S.P.; Harper, J.W. Architecture of the human interactome defines protein communities and disease networks. Nature,  2017, 545(7655), 505-509.
[http://dx.doi.org/10.1038/nature22366] [PMID: 28514442] 
[19] 
Hein, M.Y.; Hubner, N.C.; Poser, I.; Cox, J.; Nagaraj, N.; Toyoda, Y.; Gak, I.A.; Weisswange, I.; Mansfeld, J.; Buchholz, F.; Hyman, A.A.; Mann, M. A human interactome in three quantitative dimensions organized by stoichiometries and abundances. Cell,  2015, 163(3), 712-723.
[http://dx.doi.org/10.1016/j.cell.2015.09.053] [PMID: 26496610] 
[20] 
Uetz, P.; Giot, L.; Cagney, G.; Mansfield, T.A.; Judson, R.S.; Knight, J.R.; Lockshon, D.; Narayan, V.; Srinivasan, M.; Pochart, P.; Qureshi-Emili, A.; Li, Y.; Godwin, B.; Conover, D.; Kalbfleisch, T.; Vijayadamodar, G.; Yang, M.; Johnston, M.; Fields, S.; Rothberg, J.M. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature,  2000, 403(6770), 623-627.
[http://dx.doi.org/10.1038/35001009] [PMID: 10688190] 
[21] 
Kristensen, A.R.; Gsponer, J.; Foster, L.J. A high-throughput approach for measuring temporal changes in the interactome. Nat. Methods,  2012, 9(9), 907-909.
[http://dx.doi.org/10.1038/nmeth.2131] [PMID: 22863883] 
[22] 
Lee, D.S.; Park, J.; Kay, K.A.; Christakis, N.A.; Oltvai, Z.N.; Barabási, A.L. The implications of human metabolic network topology for disease comorbidity. Proc. Natl. Acad. Sci. USA,  2008, 105(29), 9880-9885.
[http://dx.doi.org/10.1073/pnas.0802208105] [PMID: 18599447] 
[23] 
Kanehisa, M.; Araki, M.; Goto, S.; Hattori, M.; Hirakawa, M.; Itoh, M.; Katayama, T.; Kawashima, S.; Okuda, S.; Tokimatsu, T.; Yamanishi, Y. KEGG for linking genomes to life and the environment. Nucleic Acids Res.,  2008, 36(Database issue), D480-D484.
[PMID: 18077471] 
[24] 
Oberhardt, M.A.; Palsson, B.O.; Papin, J.A. Applications of genome-scale metabolic reconstructions. Mol. Syst. Biol.,  2009, 5(320)
[http://dx.doi.org/10.1038/msb.2009.77] 
[25] 
Zhu, C.; Byers, K.J.; McCord, R.P.; Shi, Z.; Berger, M.F.; Newburger, D.E.; Saulrieta, K.; Smith, Z.; Shah, M.V.; Radhakrishnan, M.; Philippakis, A.A.; Hu, Y.; De Masi, F.; Pacek, M.; Rolfs, A.; Murthy, T.; Labaer, J.; Bulyk, M.L. High-resolution DNA-binding specificity analysis of yeast transcription factors. Genome Res.,  2009, 19(4), 556-566.
[http://dx.doi.org/10.1101/gr.090233.108] [PMID: 19158363] 
[26] 
Herbert A Z-DNA and z-rna in human disease. Commun. Biol.,  2019, 2(7)
[27] 
Stumpf, M.P.; Thorne, T.; de Silva, E.; Stewart, R.; An, H.J.; Lappe, M.; Wiuf, C. Estimating the size of the human interactome. Proc. Natl. Acad. Sci. USA,  2008, 105(19), 6959-6964.
[http://dx.doi.org/10.1073/pnas.0708078105] [PMID: 18474861] 
[28] 
Vidal, M. Interactome modeling. FEBS Lett.,  2005, 579(8), 1834-1838.
[http://dx.doi.org/10.1016/j.febslet.2005.02.030] [PMID: 15763560] 
[29] 
Overington, J.P.; Al-Lazikani, B.; Hopkins, A.L. How many drug targets are there? Nat. Rev. Drug Discov.,  2006, 5(12), 993-996.
[http://dx.doi.org/10.1038/nrd2199] [PMID: 17139284] 
[30] 
Santos, R.; Ursu, O.; Gaulton, A.; Bento, A.P.; Donadi, R.S.; Bologa, C.G.; Karlsson, A.; Al-Lazikani, B.; Hersey, A.; Oprea, T.I.; Overington, J.P. A comprehensive map of molecular drug targets. Nat. Rev. Drug Discov.,  2017, 16(1), 19-34.
[http://dx.doi.org/10.1038/nrd.2016.230] [PMID: 27910877] 
[31] 
Boezio, B.; Audouze, K.; Ducrot, P.; Taboureau, O. Network-based approaches in pharmacology. Mol. Inform.,  2017, 36(10)
[http://dx.doi.org/10.1002/minf.201700048] [PMID: 28692140] 
[32] 
Rosell, M.; Fernández-Recio, J. Hot-spot analysis for drug discovery targeting protein-protein interactions. Expert Opin. Drug Discov.,  2018, 13(4), 327-338.
[http://dx.doi.org/10.1080/17460441.2018.1430763] [PMID: 29376444] 
[33] 
Kim, Y.A.; Przytycka, T.M. Bridging the gap between genotype and phenotype via network approaches. Front. Genet.,  2012, 3(227)
[34] 
Stranger, B.E.; Stahl, E.A.; Raj, T. Progress and promise of genome-wide association studies for human complex trait genetics. Genetics,  2011, 187(2), 367-383.
[http://dx.doi.org/10.1534/genetics.110.120907] [PMID: 21115973] 
[35] 
Sahni, N.; Yi, S.; Taipale, M.; Fuxman Bass, J.I.; Coulombe-Huntington, J.; Yang, F.; Peng, J.; Weile, J.; Karras, G.I.; Wang, Y.; Kovács, I.A.; Kamburov, A.; Krykbaeva, I.; Lam, M.H.; Tucker, G.; Khurana, V.; Sharma, A.; Liu, Y.Y.; Yachie, N.; Zhong, Q.; Shen, Y.; Palagi, A.; San-Miguel, A.; Fan, C.; Balcha, D.; Dricot, A.; Jordan, D.M.; Walsh, J.M.; Shah, A.A.; Yang, X.; Stoyanova, A.K.; Leighton, A.; Calderwood, M.A.; Jacob, Y.; Cusick, M.E.; Salehi-Ashtiani, K.; Whitesell, L.J.; Sunyaev, S.; Berger, B.; Barabási, A.L.; Charloteaux, B.; Hill, D.E.; Hao, T.; Roth, F.P.; Xia, Y.; Walhout, A.J.M.; Lindquist, S.; Vidal, M. Widespread macromolecular interaction perturbations in human genetic disorders. Cell,  2015, 161(3), 647-660.
[http://dx.doi.org/10.1016/j.cell.2015.04.013] [PMID: 25910212] 
[36] 
Sahni, N.; Yi, S.; Zhong, Q.; Jailkhani, N.; Charloteaux, B.; Cusick, M.E.; Vidal, M. Edgotype: a fundamental link between genotype and phenotype. Curr. Opin. Genet. Dev.,  2013, 23(6), 649-657.
[http://dx.doi.org/10.1016/j.gde.2013.11.002] [PMID: 24287335] 
[37] 
Zhong, Q.; Simonis, N.; Li, Q.R.; Charloteaux, B.; Heuze, F.; Klitgord, N.; Tam, S.; Yu, H.; Venkatesan, K.; Mou, D.; Swearingen, V.; Yildirim, M.A.; Yan, H.; Dricot, A.; Szeto, D.; Lin, C.; Hao, T.; Fan, C.; Milstein, S.; Dupuy, D.; Brasseur, R.; Hill, D.E.; Cusick, M.E.; Vidal, M. Edgetic perturbation models of human inherited disorders. Mol. Syst. Biol.,  2009, 5(321)
[38] 
Cafarelli, T.M.; Desbuleux, A.; Wang, Y.; Choi, S.G.; De Ridder, D.; Vidal, M. Mapping, modeling, and characterization of protein-protein interactions on a proteomic scale. Curr. Opin. Struct. Biol.,  2017, 44, 201-210.
[http://dx.doi.org/10.1016/j.sbi.2017.05.003] 
[39] 
Lievens, S.; Vanderroost, N.; Van der Heyden, J.; Gesellchen, V.; Vidal, M.; Tavernier, J. Array MAPPIT: high-throughput interactome analysis in mammalian cells. J. Proteome Res.,  2009, 8(2), 877-886.
[http://dx.doi.org/10.1021/pr8005167] [PMID: 19159283] 
[40] 
Kühner, S.; van Noort, V.; Betts, M.J.; Leo-Macias, A.; Batisse, C.; Rode, M.; Yamada, T.; Maier, T.; Bader, S.; Beltran-Alvarez, P.; Castaño-Diez, D.; Chen, W.H.; Devos, D.; Güell, M.; Norambuena, T.; Racke, I.; Rybin, V.; Schmidt, A.; Yus, E.; Aebersold, R.; Herrmann, R.; Böttcher, B.; Frangakis, A.S.; Russell, R.B.; Serrano, L.; Bork, P.; Gavin, A.C. Proteome organization in a genome-reduced bacterium. Science,  2009, 326(5957), 1235-1240.
[http://dx.doi.org/10.1126/science.1176343] [PMID: 19965468] 
[41] 
Sevimoglu, T.; Arga, K.Y. The role of protein interaction networks in systems biomedicine. Comput. Struct. Biotechnol. J.,  2014, 11(18), 22-27.
[http://dx.doi.org/10.1016/j.csbj.2014.08.008] [PMID: 25379140] 
[42] 
Chautard, E.; Thierry-Mieg, N.; Ricard-Blum, S. Interaction networks: from protein functions to drug discovery. A review. Pathol. Biol. (Paris),  2009, 57(4), 324-333.
[http://dx.doi.org/10.1016/j.patbio.2008.10.004] [PMID: 19070972] 
[43] 
Higueruelo, A.P.; Jubb, H.; Blundell, T.L. TIMBAL v2: update of a database holding small molecules modulating protein-protein interactions. Database (Oxford),  2013, 2013, bat039
[44] 
Basse, M.J.; Betzi, S.; Bourgeas, R.; Bouzidi, S.; Chetrit, B.; Hamon, V.; Morelli, X.; Roche, P. 2P2Idb: a structural database dedicated to orthosteric modulation of protein-protein interactions. Nucleic Acids Res.,  2013, 41(Database issue), D824-D827.
[PMID: 23203891] 
[45] 
Labbé, C.M.; Kuenemann, M.A.; Zarzycka, B.; Vriend, G.; Nicolaes, G.A.; Lagorce, D.; Miteva, M.A.; Villoutreix, B.O.; Sperandio, O. iPPI-DB: an online database of modulators of protein-protein interactions. Nucleic Acids Res.,  2016, 44(D1), D542-D547.
[http://dx.doi.org/10.1093/nar/gkv982] [PMID: 26432833] 
[46] 
Chowdhury, S.; Sinha, N.; Ganguli, P.; Bhowmick, R.; Singh, V.; Nandi, S.; Sarkar, R.R. Biopydb: A dynamic human cell specific biochemical pathway database with advanced computational analyses platform. J. Integr. Bioinform.,  2018, 15(3)
[http://dx.doi.org/10.1515/jib-2017-0072] [PMID: 29547394] 
[47] 
Campbell, S.J.; Gold, N.D.; Jackson, R.M.; Westhead, D.R. Ligand binding: functional site location, similarity and docking. Curr. Opin. Struct. Biol.,  2003, 13(3), 389-395.
[http://dx.doi.org/10.1016/S0959-440X(03)00075-7] [PMID: 12831892] 
[48] 
Coleman, R.G.; Sharp, K.A. Protein pockets: inventory, shape, and comparison. J. Chem. Inf. Model.,  2010, 50(4), 589-603.
[http://dx.doi.org/10.1021/ci900397t] [PMID: 20205445] 
[49] 
Nayal, M.; Honig, B. On the nature of cavities on protein surfaces: application to the identification of drug-binding sites. Proteins,  2006, 63(4), 892-906.
[http://dx.doi.org/10.1002/prot.20897] [PMID: 16477622] 
[50] 
Levy, E.D. A simple definition of structural regions in proteins and its use in analyzing interface evolution. J. Mol. Biol.,  2010, 403(4), 660-670.
[http://dx.doi.org/10.1016/j.jmb.2010.09.028] [PMID: 20868694] 
[51] 
Ferreira, L.G.; Oliva, G.; Andricopulo, A.D. Protein-protein interaction inhibitors: advances in anticancer drug design. Expert Opin. Drug Discov.,  2016, 11(10), 957-968.
[http://dx.doi.org/10.1080/17460441.2016.1223038] [PMID: 27554357] 
[52] 
Clackson, T.; Wells, J.A. A hot spot of binding energy in a hormone-receptor interface. Science,  1995, 267(5196), 383-386.
[http://dx.doi.org/10.1126/science.7529940] [PMID: 7529940] 
[53] 
Bogan, A.A.; Thorn, K.S. Anatomy of hot spots in protein interfaces. J. Mol. Biol.,  1998, 280(1), 1-9.
[http://dx.doi.org/10.1006/jmbi.1998.1843] [PMID: 9653027] 
[54] 
Lo Conte, L.; Chothia, C.; Janin, J. The atomic structure of protein-protein recognition sites. J. Mol. Biol.,  1999, 285(5), 2177-2198.
[http://dx.doi.org/10.1006/jmbi.1998.2439] [PMID: 9925793] 
[55] 
Bahadur, R.P.; Chakrabarti, P.; Rodier, F.; Janin, J. Dissecting subunit interfaces in homodimeric proteins. Proteins,  2003, 53(3), 708-719.
[http://dx.doi.org/10.1002/prot.10461] [PMID: 14579361] 
[56] 
Chakrabarti, P.; Janin, J. Dissecting protein-protein recognition sites. Proteins,  2002, 47(3), 334-343.
[http://dx.doi.org/10.1002/prot.10085] [PMID: 11948787] 
[57] 
Moreira, I.S.; Fernandes, P.A.; Ramos, M.J. Computational alanine scanning mutagenesis--an improved methodological approach. J. Comput. Chem.,  2007, 28(3), 644-654.
[http://dx.doi.org/10.1002/jcc.20566] [PMID: 17195156] 
[58] 
Eames, M.; Kortemme, T. Structural mapping of protein interactions reveals differences in evolutionary pressures correlated to mRNA level and protein abundance. Structure,  2007, 15(11), 1442-1451.
[http://dx.doi.org/10.1016/j.str.2007.09.010] [PMID: 17997970] 
[59] 
Mintseris, J.; Weng, Z. Structure, function, and evolution of transient and obligate protein-protein interactions. Proc. Natl. Acad. Sci. USA,  2005, 102(31), 10930-10935.
[http://dx.doi.org/10.1073/pnas.0502667102] [PMID: 16043700] 
[60] 
Guharoy, M.; Chakrabarti, P. Conservation and relative importance of residues across protein-protein interfaces. Proc. Natl. Acad. Sci. USA,  2005, 102(43), 15447-15452.
[http://dx.doi.org/10.1073/pnas.0505425102] [PMID: 16221766] 
[61] 
Caffrey, D.R.; Somaroo, S.; Hughes, J.D.; Mintseris, J.; Huang, E.S. Are protein-protein interfaces more conserved in sequence than the rest of the protein surface? Protein Sci.,  2004, 13(1), 190-202.
[http://dx.doi.org/10.1110/ps.03323604] [PMID: 14691234] 
[62] 
Jones, S.; Thornton, J.M. Prediction of protein-protein interaction sites using patch analysis. J. Mol. Biol.,  1997, 272(1), 133-143.
[http://dx.doi.org/10.1006/jmbi.1997.1233] [PMID: 9299343] 
[63] 
Esmaielbeiki, R.; Krawczyk, K.; Knapp, B.; Nebel, J.C.; Deane, C.M. Progress and challenges in predicting protein interfaces. Brief. Bioinform.,  2016, 17(1), 117-131.
[http://dx.doi.org/10.1093/bib/bbv027] [PMID: 25971595] 
[64] 
Bai, F.; Morcos, F.; Cheng, R.R.; Jiang, H.; Onuchic, J.N. Elucidating the druggable interface of protein-protein interactions using fragment docking and coevolutionary analysis. Proc. Natl. Acad. Sci. USA,  2016, 113(50), E8051-E8058.
[http://dx.doi.org/10.1073/pnas.1615932113] [PMID: 27911825] 
[65] 
Harrison, R.W.; Kourinov, I.V.; Andrews, L.C. The Fourier-Green’s function and the rapid evaluation of molecular potentials. Protein Eng.,  1994, 7(3), 359-369.
[http://dx.doi.org/10.1093/protein/7.3.359] [PMID: 8177885] 
[66] 
Chen, R.; Li, L.; Weng, Z. ZDOCK: an initial-stage protein-docking algorithm. Proteins,  2003, 52(1), 80-87.
[http://dx.doi.org/10.1002/prot.10389] [PMID: 12784371] 
[67] 
Ritchie, D.W.; Kemp, G.J. Protein docking using spherical polar Fourier correlations. Proteins,  2000, 39(2), 178-194.
[http://dx.doi.org/10.1002/(SICI)1097-0134(20000501)39:2<178:AID-PROT8>3.0.CO;2-6] [PMID: 10737939] 
[68] 
Kozakov, D.; Brenke, R.; Comeau, S.R.; Vajda, S. PIPER: an FFT-based protein docking program with pairwise potentials. Proteins,  2006, 65(2), 392-406.
[http://dx.doi.org/10.1002/prot.21117] [PMID: 16933295] 
[69] 
Venkatraman, V.; Yang, Y.D.; Sael, L.; Kihara, D. Protein-protein docking using region-based 3D Zernike descriptors. BMC Bioinformatics,  2009, 10(407)
[70] 
Fischer, D.; Lin, S.L.; Wolfson, H.L.; Nussinov, R. A geometry-based suite of molecular docking processes. J. Mol. Biol.,  1995, 248(2), 459-477.
[http://dx.doi.org/10.1016/S0022-2836(95)80063-8] [PMID: 7739053] 
[71] 
Li, X.; Moal, I.H.; Bates, P.A. Detection and refinement of encounter complexes for protein-protein docking: taking account of macromolecular crowding. Proteins,  2010, 78(15), 3189-3196.
[http://dx.doi.org/10.1002/prot.22770] [PMID: 20552581] 
[72] 
Gardiner, E.J.; Willett, P.; Artymiuk, P.J. Gapdock: A genetic algorithm approach to protein docking in capri round 1. Proteins,  2003, 52(1), 10-14.
[http://dx.doi.org/10.1002/prot.10386] [PMID: 12784360] 
[73] 
Gray, J.J.; Moughon, S.; Wang, C.; Schueler-Furman, O.; Kuhlman, B.; Rohl, C.A.; Baker, D. Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. J. Mol. Biol.,  2003, 331(1), 281-299.
[http://dx.doi.org/10.1016/S0022-2836(03)00670-3] [PMID: 12875852] 
[74] 
Douguet, D.; Chen, H.C.; Tovchigrechko, A.; Vakser, I.A. DOCKGROUND resource for studying protein-protein interfaces. Bioinformatics,  2006, 22(21), 2612-2618.
[http://dx.doi.org/10.1093/bioinformatics/btl447] [PMID: 16928732] 
[75] 
Gao, Y.; Douguet, D.; Tovchigrechko, A.; Vakser, I.A. DOCKGROUND system of databases for protein recognition studies: unbound structures for docking. Proteins,  2007, 69(4), 845-851.
[http://dx.doi.org/10.1002/prot.21714] [PMID: 17803215] 
[76] 
Hwang, H.; Vreven, T.; Janin, J.; Weng, Z. Protein-protein docking benchmark version 4.0. Proteins,  2010, 78(15), 3111-3114.
[http://dx.doi.org/10.1002/prot.22830] [PMID: 20806234] 
[77] 
Kundrotas, P.J.; Anishchenko, I.; Dauzhenka, T.; Kotthoff, I.; Mnevets, D.; Copeland, M.M.; Vakser, I.A. Dockground: A comprehensive data resource for modeling of protein complexes. Protein Sci.,  2018, 27(1), 172-181.
[http://dx.doi.org/10.1002/pro.3295] [PMID: 28891124] 
[78] 
Ruvinsky, A.M.; Kirys, T.; Tuzikov, A.V.; Vakser, I.A. Side-chain conformational changes upon Protein-Protein Association. J. Mol. Biol.,  2011, 408(2), 356-365.
[http://dx.doi.org/10.1016/j.jmb.2011.02.030] [PMID: 21354429] 
[79] 
Andrusier, N.; Mashiach, E.; Nussinov, R.; Wolfson, H.J. Principles of flexible protein-protein docking. Proteins,  2008, 73(2), 271-289.
[http://dx.doi.org/10.1002/prot.22170] [PMID: 18655061] 
[80] 
O’Toole, N.; Vakser, I.A. Large-scale characteristics of the energy landscape in protein-protein interactions. Proteins,  2008, 71(1), 144-152.
[http://dx.doi.org/10.1002/prot.21665] [PMID: 17932937] 
[81] 
Ruvinsky, A.M.; Vakser, I.A. Interaction cutoff effect on ruggedness of protein-protein energy landscape. Proteins,  2008, 70(4), 1498-1505.
[http://dx.doi.org/10.1002/prot.21644] [PMID: 17910068] 
[82] 
Vakser, I.A. Protein-protein docking: from interaction to interactome. Biophys. J.,  2014, 107(8), 1785-1793.
[http://dx.doi.org/10.1016/j.bpj.2014.08.033] [PMID: 25418159] 
[83] 
Beglov, D.; Hall, D.R.; Brenke, R.; Shapovalov, M.V.; Dunbrack, R.L., Jr; Kozakov, D.; Vajda, S. Minimal ensembles of side chain conformers for modeling protein-protein interactions. Proteins,  2012, 80(2), 591-601.
[http://dx.doi.org/10.1002/prot.23222] [PMID: 22105850] 
[84] 
Kirys, T.; Ruvinsky, A.M.; Tuzikov, A.V.; Vakser, I.A. Rotamer libraries and probabilities of transition between rotamers for the side chains in protein-protein binding. Proteins,  2012, 80(8), 2089-2098.
[http://dx.doi.org/10.1002/prot.24103] [PMID: 22544766] 
[85] 
Chothia, C.; Janin, J. Principles of protein-protein recognition. Nature,  1975, 256(5520), 705-708.
[http://dx.doi.org/10.1038/256705a0] [PMID: 1153006] 
[86] 
Tuncbag, N.; Gursoy, A.; Keskin, O. Prediction of protein-protein interactions: unifying evolution and structure at protein interfaces. Phys. Biol.,  2011, 8(3), 035006
[http://dx.doi.org/10.1088/1478-3975/8/3/035006] [PMID: 21572173] 
[87] 
Guerler, A.; Govindarajoo, B.; Zhang, Y. Mapping monomeric threading to protein-protein structure prediction. J. Chem. Inf. Model.,  2013, 53(3), 717-725.
[http://dx.doi.org/10.1021/ci300579r] [PMID: 23413988] 
[88] 
Singh, R; Park, D; Xu, J; Hosur, R Berger B Struct2net: A web service to predict protein-protein interactions using a structure-based approach. Nucleic Acids Res,  2010, 38(Web Server issue), W508-515.
[89] 
Aloy, P.; Ceulemans, H.; Stark, A.; Russell, R.B. The relationship between sequence and interaction divergence in proteins. J. Mol. Biol.,  2003, 332(5), 989-998.
[http://dx.doi.org/10.1016/j.jmb.2003.07.006] [PMID: 14499603] 
[90] 
Yu, H.; Luscombe, N.M.; Lu, H.X.; Zhu, X.; Xia, Y.; Han, J.D.; Bertin, N.; Chung, S.; Vidal, M.; Gerstein, M. Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs. Genome Res.,  2004, 14(6), 1107-1118.
[http://dx.doi.org/10.1101/gr.1774904] [PMID: 15173116] 
[91] 
Mintseris, J.; Pierce, B.; Wiehe, K.; Anderson, R.; Chen, R.; Weng, Z. Integrating statistical pair potentials into protein complex prediction. Proteins,  2007, 69(3), 511-520.
[http://dx.doi.org/10.1002/prot.21502] [PMID: 17623839] 
[92] 
Li, B.; Kihara, D. Protein docking prediction using predicted protein-protein interface. BMC Bioinformatics,  2012, 13(7)
[http://dx.doi.org/10.1186/1471-2105-13-7] 
[93] 
Ezkurdia, I.; Bartoli, L.; Fariselli, P.; Casadio, R.; Valencia, A.; Tress, M.L. Progress and challenges in predicting protein-protein interaction sites. Brief. Bioinform.,  2009, 10(3), 233-246.
[http://dx.doi.org/10.1093/bib/bbp021] [PMID: 19346321] 
[94] 
Ofran, Y.; Rost, B. ISIS: interaction sites identified from sequence. Bioinformatics,  2007, 23(2), e13-e16.
[http://dx.doi.org/10.1093/bioinformatics/btl303] [PMID: 17237081] 
[95] 
Rost, B. Review: protein secondary structure prediction continues to rise. J. Struct. Biol.,  2001, 134(2-3), 204-218.
[http://dx.doi.org/10.1006/jsbi.2001.4336] [PMID: 11551180] 
[96] 
Shen, J.; Zhang, J.; Luo, X.; Zhu, W.; Yu, K.; Chen, K.; Li, Y.; Jiang, H. Predicting protein-protein interactions based only on sequences information. Proc. Natl. Acad. Sci. USA,  2007, 104(11), 4337-4341.
[http://dx.doi.org/10.1073/pnas.0607879104] [PMID: 17360525] 
[97] 
Baspinar, A; Cukuroglu, E; Nussinov, R; Keskin, O Gursoy A
 Prism: A web server and repository for prediction of proteinprotein
 interactions and modeling their 3d complexes. Nucleic
 Acids Res,  2014, 42(Web Server issue), W285-289.
[98] 
Porollo, A.; Meller, J. Prediction-based fingerprints of protein-protein interactions. Proteins,  2007, 66(3), 630-645.
[http://dx.doi.org/10.1002/prot.21248] [PMID: 17152079] 
[99] 
Koike, A.; Takagi, T. Prediction of protein-protein interaction sites using support vector machines. Protein Eng. Des. Sel.,  2004, 17(2), 165-173.
[http://dx.doi.org/10.1093/protein/gzh020] [PMID: 15047913] 
[100] 
Zhou, H.X.; Shan, Y. Prediction of protein interaction sites from sequence profile and residue neighbor list. Proteins,  2001, 44(3), 336-343.
[http://dx.doi.org/10.1002/prot.1099] [PMID: 11455607] 
[101] 
Fariselli, P.; Pazos, F.; Valencia, A.; Casadio, R. Prediction of protein--protein interaction sites in heterocomplexes with neural networks. Eur. J. Biochem.,  2002, 269(5), 1356-1361.
[http://dx.doi.org/10.1046/j.1432-1033.2002.02767.x] [PMID: 11874449] 
[102] 
Ofran, Y.; Rost, B. Predicted protein-protein interaction sites from local sequence information. FEBS Lett.,  2003, 544(1-3), 236-239.
[http://dx.doi.org/10.1016/S0014-5793(03)00456-3] [PMID: 12782323] 
[103] 
Chowdhary, R.; Zhang, J.; Liu, J.S. Bayesian inference of protein-protein interactions from biological literature. Bioinformatics,  2009, 25(12), 1536-1542.
[http://dx.doi.org/10.1093/bioinformatics/btp245] [PMID: 19369495] 
[104] 
Jansen, R.; Yu, H.; Greenbaum, D.; Kluger, Y.; Krogan, N.J.; Chung, S.; Emili, A.; Snyder, M.; Greenblatt, J.F.; Gerstein, M. A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science,  2003, 302(5644), 449-453.
[http://dx.doi.org/10.1126/science.1087361] [PMID: 14564010] 
[105] 
Neuvirth, H.; Raz, R.; Schreiber, G. ProMate: a structure based prediction program to identify the location of protein-protein binding sites. J. Mol. Biol.,  2004, 338(1), 181-199.
[http://dx.doi.org/10.1016/j.jmb.2004.02.040] [PMID: 15050833] 
[106] 
Li, H.; Gong, X.J.; Yu, H.; Zhou, C. Deep neural network based predictions of protein interactions using primary sequences. Molecules,  2018, 23(8), E1923
[http://dx.doi.org/10.3390/molecules23081923] [PMID: 30071670] 
[107] 
Du, X.; Sun, S.; Hu, C.; Yao, Y.; Yan, Y.; Zhang, Y. Deepppi: Boosting prediction of protein-protein interactions with deep neural networks. J. Chem. Inf. Model.,  2017, 57(6), 1499-1510.
[http://dx.doi.org/10.1021/acs.jcim.7b00028] [PMID: 28514151] 
[108] 
Skwark, M.J.; Raimondi, D.; Michel, M.; Elofsson, A. Improved contact predictions using the recognition of protein like contact patterns. PLOS Comput. Biol.,  2014, 10(11), e1003889
[http://dx.doi.org/10.1371/journal.pcbi.1003889] [PMID: 25375897] 
[109] 
Sun, T.; Zhou, B.; Lai, L.; Pei, J. Sequence-based prediction of protein protein interaction using a deep-learning algorithm. BMC Bioinformatics,  2017, 18(1), 277.
[http://dx.doi.org/10.1186/s12859-017-1700-2] [PMID: 28545462] 
[110] 
Hopf, T.A.; Schärfe, C.P.; Rodrigues, J.P.; Green, A.G.; Kohlbacher, O.; Sander, C.; Bonvin, A.M.; Marks, D.S. Sequence co-evolution gives 3D contacts and structures of protein complexes. eLife,  2014, 3, 3.
[http://dx.doi.org/10.7554/eLife.03430] [PMID: 25255213] 
[111] 
Halabi, N.; Rivoire, O.; Leibler, S.; Ranganathan, R. Protein sectors: evolutionary units of three-dimensional structure. Cell,  2009, 138(4), 774-786.
[http://dx.doi.org/10.1016/j.cell.2009.07.038] [PMID: 19703402] 
[112] 
dos Santos, R.N.; Morcos, F.; Jana, B.; Andricopulo, A.D.; Onuchic, J.N. Dimeric interactions and complex formation using direct coevolutionary couplings. Sci. Rep.,  2015, 5(1), 13652.
[http://dx.doi.org/10.1038/srep13652] 
[113] 
Kaján, L.; Hopf, T.A.; Kalaš, M.; Marks, D.S.; Rost, B. FreeContact: fast and free software for protein contact prediction from residue co-evolution. BMC Bioinformatics,  2014, 15(85)
[114] 
Glaser, F.; Pupko, T.; Paz, I.; Bell, R.E.; Bechor-Shental, D.; Martz, E.; Ben-Tal, N. ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information. Bioinformatics,  2003, 19(1), 163-164.
[http://dx.doi.org/10.1093/bioinformatics/19.1.163] [PMID: 12499312] 
[115] 
Jones, D.T.; Buchan, D.W.; Cozzetto, D.; Pontil, M. PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments. Bioinformatics,  2012, 28(2), 184-190.
[http://dx.doi.org/10.1093/bioinformatics/btr638] [PMID: 22101153] 
[116] 
Smith, M.C.; Gestwicki, J.E. Features of protein-protein interactions that translate into potent inhibitors: topology, surface area and affinity. Expert Rev. Mol. Med.,  2012, 14, e16
[117] 
Bahadur, R.P.; Chakrabarti, P.; Rodier, F.; Janin, J. A dissection of specific and non-specific protein-protein interfaces. J. Mol. Biol.,  2004, 336(4), 943-955.
[http://dx.doi.org/10.1016/j.jmb.2003.12.073] [PMID: 15095871] 
[118] 
Si, Y.; Xu, D.; Bum-Erdene, K.; Ghozayel, M.K.; Yang, B.; Clemons, P.A.; Meroueh, S.O. Chemical space overlap with critical protein-protein interface residues in commercial and specialized small-molecule libraries. ChemMedChem,  2019, 14(1), 119-131.
[PMID: 30548204] 
[119] 
Arkin, M.R.; Tang, Y.; Wells, J.A. Small-molecule inhibitors of protein-protein interactions: progressing toward the reality. Chem. Biol.,  2014, 21(9), 1102-1114.
[http://dx.doi.org/10.1016/j.chembiol.2014.09.001] [PMID: 25237857] 
[120] 
Cheng, R.R.; Morcos, F.; Levine, H.; Onuchic, J.N. Toward rationally redesigning bacterial two-component signaling systems using coevolutionary information. Proc. Natl. Acad. Sci. USA,  2014, 111(5), E563-E571.
[http://dx.doi.org/10.1073/pnas.1323734111] [PMID: 24449878] 
[121] 
Eisenberg, D.; Weiss, R.M.; Terwilliger, T.C. The helical hydrophobic moment: a measure of the amphiphilicity of a helix. Nature,  1982, 299(5881), 371-374.
[http://dx.doi.org/10.1038/299371a0] [PMID: 7110359] 
[122] 
Gallet, X.; Charloteaux, B.; Thomas, A.; Brasseur, R. A fast method to predict protein interaction sites from sequences. J. Mol. Biol.,  2000, 302(4), 917-926.
[http://dx.doi.org/10.1006/jmbi.2000.4092] [PMID: 10993732] 
[123] 
Ahmad, S.; Mizuguchi, K. Partner-aware prediction of interacting residues in protein-protein complexes from sequence data. PLoS One,  2011, 6(12), e29104
[http://dx.doi.org/10.1371/journal.pone.0029104] [PMID: 22194998] 
[124] 
Jia, J.; Liu, Z.; Xiao, X.; Liu, B.; Chou, K.C  Ippi-esml: An ensemble classifier for identifying the interactions of proteins by incorporating their physicochemical properties and wavelet transforms into pseaac. J. Theor. Biol.,  2015, 377, 47-56.
[125] 
Jia, J.; Liu, Z.; Xiao, X.; Liu, B.; Chou, K.C. Identification of protein-protein binding sites by incorporating the physicochemical properties and stationary wavelet transforms into pseudo amino acid composition. J. Biomol. Struct. Dyn.,  2016, 34(9), 1946-1961.
[http://dx.doi.org/10.1080/07391102.2015.1095116] [PMID: 26375780] 
[126] 
Bendell, C.J.; Liu, S.; Aumentado-Armstrong, T.; Istrate, B.; Cernek, P.T.; Khan, S.; Picioreanu, S.; Zhao, M.; Murgita, R.A. Transient protein-protein interface prediction: datasets, features, algorithms, and the RAD-T predictor. BMC Bioinformatics,  2014, 15(82)
[127] 
Boyen, P.; Van Dyck, D.; Neven, F.; van Ham, R.C.; van Dijk, A.D. SLIDER: a generic metaheuristic for the discovery of correlated motifs in protein-protein interaction networks. IEEE/ACM Trans. Comput. Biol. Bioinformatics,  2011, 8(5), 1344-1357.
[http://dx.doi.org/10.1109/TCBB.2011.17] [PMID: 21282865] 
[128] 
Tamir, S.; Rotem-Bamberger, S.; Katz, C.; Morcos, F.; Hailey, K.L.; Zuris, J.A.; Wang, C.; Conlan, A.R.; Lipper, C.H.; Paddock, M.L.; Mittler, R.; Onuchic, J.N.; Jennings, P.A.; Friedler, A.; Nechushtai, R. Integrated strategy reveals the protein interface between cancer targets Bcl-2 and NAF-1. Proc. Natl. Acad. Sci. USA,  2014, 111(14), 5177-5182.
[http://dx.doi.org/10.1073/pnas.1403770111] [PMID: 24706857] 
[129] 
Lichtarge, O.; Bourne, H.R.; Cohen, F.E. An evolutionary trace method defines binding surfaces common to protein families. J. Mol. Biol.,  1996, 257(2), 342-358.
[http://dx.doi.org/10.1006/jmbi.1996.0167] [PMID: 8609628] 
[130] 
Zellner, H.; Staudigel, M.; Trenner, T.; Bittkowski, M.; Wolowski, V.; Icking, C.; Merkl, R. PresCont: predicting protein-protein interfaces utilizing four residue properties. Proteins,  2012, 80(1), 154-168.
[http://dx.doi.org/10.1002/prot.23172] [PMID: 22038731] 
[131] 
Yang, Y.; Gong, X. A new probability method to understand protein-protein interface formation mechanism at amino acid level. J. Theor. Biol.,  2018, 436, 18-25.
[132] 
Luo, X.; You, Z.; Zhou, M.; Li, S.; Leung, H.; Xia, Y.; Zhu, Q. A highly efficient approach to protein interactome mapping based on collaborative filtering framework. Sci. Rep.,  2015, 5(7702)
[133] 
Shoemaker, B.A.; Zhang, D.; Thangudu, R.R.; Tyagi, M.; Fong, J.H.; Marchler-Bauer, A.; Bryant, S.H.; Madej, T.; Panchenko, A.R. Inferred Biomolecular Interaction Server--a web server to analyze and predict protein interacting partners and binding sites. Nucleic Acids Res.,  2010, 38(Database issue), D518-D524.
[http://dx.doi.org/10.1093/nar/gkp842] [PMID: 19843613] 
[134] 
Shoemaker, B.A.; Zhang, D.; Tyagi, M.; Thangudu, R.R.; Fong, J.H.; Marchler-Bauer, A.; Bryant, S.H.; Madej, T.; Panchenko, A.R. IBIS (Inferred Biomolecular Interaction Server) reports, predicts and integrates multiple types of conserved interactions for proteins. Nucleic Acids Res.,  2012, 40(Database issue), D834-D840.
[http://dx.doi.org/10.1093/nar/gkr997] [PMID: 22102591] 
[135] 
Russell, R.B.; Sasieni, P.D.; Sternberg, M.J. Supersites within superfolds. Binding site similarity in the absence of homology. J. Mol. Biol.,  1998, 282(4), 903-918.
[http://dx.doi.org/10.1006/jmbi.1998.2043] [PMID: 9743635] 
[136] 
Brylinski, M.; Skolnick, J. FINDSITE: a threading-based approach to ligand homology modeling. PLOS Comput. Biol.,  2009, 5(6), e1000405
[http://dx.doi.org/10.1371/journal.pcbi.1000405] [PMID: 19503616] 
[137] 
Jordan, R.A.; El-Manzalawy, Y.; Dobbs, D.; Honavar, V. Predicting protein-protein interface residues using local surface structural similarity. BMC Bioinformatics,  2012, 13, 41.
[http://dx.doi.org/10.1186/1471-2105-13-41] 
[138] 
Zhang, Q.C.; Petrey, D.; Norel, R.; Honig, B.H. Protein interface conservation across structure space. Proc. Natl. Acad. Sci. USA,  2010, 107(24), 10896-10901.
[http://dx.doi.org/10.1073/pnas.1005894107] [PMID: 20534496] 
[139] 
Zhang, QC; Deng, L; Fisher, M; Guan, J; Honig, B Petrey D Predus: A web server for predicting protein interfaces using structural neighbors. Nucleic Acids Res.,  2011, 39(Web Server
 issue), W283-287.
[140] 
Fischer, M; Zhang, QC; Dey, F; Chen, BY; Honig, B Petrey D Markus: A server to navigate sequence-structure-function space. Nucleic Acids Res.,  2011, 39(Web Server issue), W357-361.
[141] 
Minhas, Fu.; Geiss, B.J.; Ben-Hur, A. PAIRpred: partner-specific prediction of interacting residues from sequence and structure. Proteins,  2014, 82(7), 1142-1155.
[http://dx.doi.org/10.1002/prot.24479] [PMID: 24243399] 
[142] 
Hwang, H.; Vreven, T.; Weng, Z. Binding interface prediction by combining protein-protein docking results. Proteins,  2014, 82(1), 57-66.
[http://dx.doi.org/10.1002/prot.24354] [PMID: 23836482] 
[143] 
de Juan, D.; Pazos, F.; Valencia, A. Emerging methods in protein co-evolution. Nat. Rev. Genet.,  2013, 14(4), 249-261.
[http://dx.doi.org/10.1038/nrg3414] [PMID: 23458856] 
[144] 
Marrero, M.; Immink, R.; de Ridder, D.; van Dijk, A. Improved inference of intermolecular contacts through protein-protein interaction prediction using coevolutionary analysis. Bioinformatics,  2018, 35(12), 2036-2042.
[145] 
Pazos, F.; Helmer-Citterich, M.; Ausiello, G.; Valencia, A. Correlated mutations contain information about protein-protein interaction. J. Mol. Biol.,  1997, 271(4), 511-523.
[http://dx.doi.org/10.1006/jmbi.1997.1198] [PMID: 9281423] 
[146] 
Segura, J.; Jones, P.F.; Fernandez-Fuentes, N. Improving the prediction of protein binding sites by combining heterogeneous data and Voronoi diagrams. BMC Bioinformatics,  2011, 12(352)
[http://dx.doi.org/10.1186/1471-2105-12-352] 
[147] 
Segura, J.; Jones, P.F.; Fernandez-Fuentes, N. A holistic in silico approach to predict functional sites in protein structures. Bioinformatics,  2012, 28(14), 1845-1850.
[http://dx.doi.org/10.1093/bioinformatics/bts269] [PMID: 22563069] 
[148] 
Schymkowitz, J; Borg, J; Stricher, F; Nys, R; Rousseau, F; Serrano, L L The foldx web server: An online force field. Nucleic Acids Res,  2005, 33(Web Server issue), W382-388.
[149] 
Lise, S.; Buchan, D.; Pontil, M.; Jones, D.T. Predictions of hot spot residues at protein-protein interfaces using support vector machines. PLoS One,  2011, 6(2), e16774
[http://dx.doi.org/10.1371/journal.pone.0016774] [PMID: 21386962] 
[150] 
Kim, DE; Chivian, D; Baker, D Protein structure prediction and analysis using the robetta server. Nucleic Acids Res,  2004, 32(Web
 Server issue), W526-531.
[http://dx.doi.org/10.1093/nar/gkh468] 
[151] 
Kruger, DM; Gohlke, H Drugscoreppi webserver: Fast and accurate
 in silico alanine scanning for scoring protein-protein interactions. Nucleic Acids Res,  2010, 38(Web Server issue), W480-486.
[152] 
Deng, L; Zhang, QC; Chen, Z; Meng, Y; Guan, J; Zhou, S Predhs: A web server for predicting protein-protein interaction hot spots by using structural neighborhood properties. Nucleic Acids Res,  2014, 42(Web Server issue), W290-295.
[153] 
Deng, L.; Guan, J.; Wei, X.; Yi, Y.; Zhang, Q.C.; Zhou, S. Boosting prediction performance of protein-protein interaction hot spots by using structural neighborhood properties. J. Comput. Biol.,  2013, 20(11), 878-891.
[http://dx.doi.org/10.1089/cmb.2013.0083] [PMID: 24134392] 
[154] 
Gao, Y.; Wang, R.; Lai, L. Structure-based method for analyzing protein-protein interfaces. J. Mol. Model.,  2004, 10(1), 44-54.
[http://dx.doi.org/10.1007/s00894-003-0168-3] [PMID: 14634848] 
[155] 
Cukuroglu, E.; Engin, H.B.; Gursoy, A.; Keskin, O. Hot spots in protein-protein interfaces: towards drug discovery. Prog. Biophys. Mol. Biol.,  2014, 116(2-3), 165-173.
[http://dx.doi.org/10.1016/j.pbiomolbio.2014.06.003] [PMID: 24997383] 
[156] 
Segura Mora, J.; Assi, S.A.; Fernandez-Fuentes, N. Presaging critical residues in protein interfaces-web server (PCRPi-W): a web server to chart hot spots in protein interfaces. PLoS One,  2010, 5(8), e12352
[http://dx.doi.org/10.1371/journal.pone.0012352] [PMID: 20808810] 
[157] 
Koes, DR; Camacho, CJ Pocketquery: Protein-protein interaction
 inhibitor starting points from protein-protein interaction structure. Nucleic Acids Res,  2012, 40(Web Server issue), W387-392.
[158] 
Darnell, SJ; LeGault, L Mitchell, JC Kfc server: Interactive
 forecasting of protein interaction hot spots. Nucleic Acids Res,  2008, 36(Web Server issue), W265-269.
[159] 
Zhu, X.; Mitchell, J.C. KFC2: a knowledge-based hot spot prediction method based on interface solvation, atomic density, and plasticity features. Proteins,  2011, 79(9), 2671-2683.
[http://dx.doi.org/10.1002/prot.23094] [PMID: 21735484] 
[160] 
Qiao, Y.; Xiong, Y.; Gao, H.; Zhu, X.; Chen, P. Protein-protein interface hot spots prediction based on a hybrid feature selection strategy. BMC Bioinformatics,  2018, 19(1), 14.
[http://dx.doi.org/10.1186/s12859-018-2009-5] [PMID: 29334889] 
[161] 
Tuncbag, N.; Gursoy, A.; Keskin, O. Identification of computational hot spots in protein interfaces: combining solvent accessibility and inter-residue potentials improves the accuracy. Bioinformatics,  2009, 25(12), 1513-1520.
[http://dx.doi.org/10.1093/bioinformatics/btp240] [PMID: 19357097] 
[162] 
Tuncbag, N; Keskin, O Gursoy A Hotpoint: Hot spot prediction
 server for protein interfaces. Nucleic Acids Res,  2010, 38(Web
 Server issue), W402-406.
[163] 
Bourgeas, R.; Basse, M.J.; Morelli, X.; Roche, P. Atomic analysis of protein-protein interfaces with known inhibitors: the 2P2I database. PLoS One,  2010, 5(3), e9598
[http://dx.doi.org/10.1371/journal.pone.0009598] [PMID: 20231898] 
[164] 
Rooklin, D.; Wang, C.; Katigbak, J.; Arora, P.S.; Zhang, Y. Alphaspace: Fragment-centric topographical mapping to target protein-protein interaction interfaces. J. Chem. Inf. Model.,  2015, 55(8), 1585-1599.
[http://dx.doi.org/10.1021/acs.jcim.5b00103] [PMID: 26225450] 
[165] 
Laurie, A.T.; Jackson, R.M. Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites. Bioinformatics,  2005, 21(9), 1908-1916.
[http://dx.doi.org/10.1093/bioinformatics/bti315] [PMID: 15701681] 
[166] 
Lasagni, L.; Francalanci, M.; Annunziato, F.; Lazzeri, E.; Giannini, S.; Cosmi, L.; Sagrinati, C.; Mazzinghi, B.; Orlando, C.; Maggi, E.; Marra, F.; Romagnani, S.; Serio, M.; Romagnani, P. An alternatively spliced variant of CXCR3 mediates the inhibition of endothelial cell growth induced by IP-10, Mig, and I-TAC, and acts as functional receptor for platelet factor 4. J. Exp. Med.,  2003, 197(11), 1537-1549.
[http://dx.doi.org/10.1084/jem.20021897] [PMID: 12782716] 
[167] 
Bodnar, R.J.; Yates, C.C.; Rodgers, M.E.; Du, X.; Wells, A. IP-10 induces dissociation of newly formed blood vessels. J. Cell Sci.,  2009, 122(Pt 12), 2064-2077.
[http://dx.doi.org/10.1242/jcs.048793] [PMID: 19470579] 
[168] 
Zlotnik, A.; Yoshie, O. Chemokines: a new classification system and their role in immunity. Immunity,  2000, 12(2), 121-127.
[http://dx.doi.org/10.1016/S1074-7613(00)80165-X] [PMID: 10714678] 
[169] 
Burg, J.S.; Ingram, J.R.; Venkatakrishnan, A.J.; Jude, K.M.; Dukkipati, A.; Feinberg, E.N.; Angelini, A.; Waghray, D.; Dror, R.O.; Ploegh, H.L.; Garcia, K.C. Structural biology. Structural basis for chemokine recognition and activation of a viral G protein-coupled receptor. Science,  2015, 347(6226), 1113-1117.
[http://dx.doi.org/10.1126/science.aaa5026] [PMID: 25745166] 
[170] 
Scheerer, P.; Park, J.H.; Hildebrand, P.W.; Kim, Y.J.; Krauss, N.; Choe, H.W.; Hofmann, K.P.; Ernst, O.P. Crystal structure of opsin in its G-protein-interacting conformation. Nature,  2008, 455(7212), 497-502.
[http://dx.doi.org/10.1038/nature07330] [PMID: 18818650] 
[171] 
Qin, L.; Kufareva, I.; Holden, L.G.; Wang, C.; Zheng, Y.; Zhao, C.; Fenalti, G.; Wu, H.; Han, G.W.; Cherezov, V.; Abagyan, R.; Stevens, R.C.; Handel, T.M. Structural biology. Crystal structure of the chemokine receptor CXCR4 in complex with a viral chemokine. Science,  2015, 347(6226), 1117-1122.
[http://dx.doi.org/10.1126/science.1261064] [PMID: 25612609] 
[172] 
Wu, B.; Chien, E.Y.; Mol, C.D.; Fenalti, G.; Liu, W.; Katritch, V.; Abagyan, R.; Brooun, A.; Wells, P.; Bi, F.C.; Hamel, D.J.; Kuhn, P.; Handel, T.M.; Cherezov, V.; Stevens, R.C. Structures of the CXCR4 chemokine GPCR with small-molecule and cyclic peptide antagonists. Science,  2010, 330(6007), 1066-1071.
[http://dx.doi.org/10.1126/science.1194396] [PMID: 20929726] 
[173] 
Chen, R.; Weng, Z. A novel shape complementarity scoring function for protein-protein docking. Proteins,  2003, 51(3), 397-408.
[http://dx.doi.org/10.1002/prot.10334] [PMID: 12696051] 
[174] 
Oughtred, R.; Stark, C.; Breitkreutz, B.J.; Rust, J.; Boucher, L.; Chang, C.; Kolas, N.; O’Donnell, L.; Leung, G.; McAdam, R.; Zhang, F.; Dolma, S.; Willems, A.; Coulombe-Huntington, J.; Chatr-Aryamontri, A.; Dolinski, K.; Tyers, M. The BioGRID interaction database: 2019 update. Nucleic Acids Res.,  2019, 47(D1), D529-D541.
[http://dx.doi.org/10.1093/nar/gky1079] [PMID: 30476227] 
[175] 
Marchler-Bauer, A; Bryant, SH Cd-search: Protein domain
 annotations on the fly. Nucleic Acids Res.,  2004, 32(Web Server
 issue), W327-331.
[176] 
Giurgiu, M.; Reinhard, J.; Brauner, B.; Dunger-Kaltenbach, I.; Fobo, G.; Frishman, G.; Montrone, C.; Ruepp, A. CORUM: the comprehensive resource of mammalian protein complexes-2019. Nucleic Acids Res.,  2019, 47(D1), D559-D563.
[http://dx.doi.org/10.1093/nar/gky973] [PMID: 30357367] 
[177] 
Pu, S.; Vlasblom, J.; Emili, A.; Greenblatt, J.; Wodak, S.J. Identifying functional modules in the physical interactome of Saccharomyces cerevisiae. Proteomics,  2007, 7(6), 944-960.
[http://dx.doi.org/10.1002/pmic.200600636] [PMID: 17370254] 
[178] 
Pu, S.; Wong, J.; Turner, B.; Cho, E.; Wodak, S.J. Up-to-date catalogues of yeast protein complexes. Nucleic Acids Res.,  2009, 37(3), 825-831.
[http://dx.doi.org/10.1093/nar/gkn1005] [PMID: 19095691] 
[179] 
Xenarios, I.; Rice, D.W.; Salwinski, L.; Baron, M.K.; Marcotte, E.M.; Eisenberg, D. DIP: the database of interacting proteins. Nucleic Acids Res.,  2000, 28(1), 289-291.
[http://dx.doi.org/10.1093/nar/28.1.289] [PMID: 10592249] 
[180] 
Xenarios, I.; Fernandez, E.; Salwinski, L.; Duan, X.J.; Thompson, M.J.; Marcotte, E.M.; Eisenberg, D. Dip: The database of interacting proteins: 2001 update. Nucleic Acids Res.,  2001, 29(1), 239-241.
[http://dx.doi.org/10.1093/nar/29.1.239] [PMID: 11125102] 
[181] 
Xenarios, I.; Salwínski, L.; Duan, X.J.; Higney, P.; Kim, S.M.; Eisenberg, D. DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions. Nucleic Acids Res.,  2002, 30(1), 303-305.
[http://dx.doi.org/10.1093/nar/30.1.303] [PMID: 11752321] 
[182] 
Salwinski, L.; Miller, C.S.; Smith, A.J.; Pettit, F.K.; Bowie, J.U.; Eisenberg, D. The database of interacting proteins: 2004 update. Nucleic Acids Res.,  2004, 32(Database issue), D449-D451.
[http://dx.doi.org/10.1093/nar/gkh086] [PMID: 14681454] 
[183] 
Kuang, X.; Han, J.G.; Zhao, N.; Pang, B.; Shyu, C.R.; Korkin, D. DOMMINO: a database of macromolecular interactions. Nucleic Acids Res.,  2012, 40(Database issue), D501-D506.
[http://dx.doi.org/10.1093/nar/gkr1128] [PMID: 22135305] 
[184] 
Kundrotas, P.J.; Zhu, Z.; Vakser, I.A. GWIDD: Genome-wide protein docking database. Nucleic Acids Res.,  2010, 38(Database issue), D513-D517.
[http://dx.doi.org/10.1093/nar/gkp944] [PMID: 19900970] 
[185] 
López, Y.; Nakai, K.; Patil, A. HitPredict version 4: comprehensive reliability scoring of physical protein-protein interactions from more than 100 species. Database (Oxford),  2015, 2015,pii: bav117
[186] 
Patil, A.; Nakai, K.; Nakamura, H. HitPredict: a database of quality assessed protein-protein interactions in nine species. Nucleic Acids Res.,  2011, 39(Database issue), D744-D749.
[http://dx.doi.org/10.1093/nar/gkq897] [PMID: 20947562] 
[187] 
Orchard, S.; Ammari, M.; Aranda, B.; Breuza, L.; Briganti, L.; Broackes-Carter, F.; Campbell, N.H.; Chavali, G.; Chen, C.; del-Toro, N.; Duesbury, M.; Dumousseau, M.; Galeota, E.; Hinz, U.; Iannuccelli, M.; Jagannathan, S.; Jimenez, R.; Khadake, J.; Lagreid, A.; Licata, L.; Lovering, R.C.; Meldal, B.; Melidoni, A.N.; Milagros, M.; Peluso, D.; Perfetto, L.; Porras, P.; Raghunath, A.; Ricard-Blum, S.; Roechert, B.; Stutz, A.; Tognolli, M.; van Roey, K.; Cesareni, G.; Hermjakob, H. The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases. Nucleic Acids Res.,  2014, 42(Database issue), D358-D363.
[http://dx.doi.org/10.1093/nar/gkt1115] [PMID: 24234451] 
[188] 
Razick, S.; Magklaras, G.; Donaldson, I.M. iRefIndex: a consolidated protein interaction database with provenance. BMC Bioinformatics,  2008, 9, 405.
[189] 
Park, D.; Singh, R.; Baym, M.; Liao, C.S.; Berger, B. IsoBase: a database of functionally related proteins across PPI networks. Nucleic Acids Res.,  2011, 39(Database issue), D295-D300.
[http://dx.doi.org/10.1093/nar/gkq1234] [PMID: 21177658] 
[190] 
Singh, R.; Xu, J.; Berger, B. Global alignment of multiple protein interaction networks with application to functional orthology detection. Proc. Natl. Acad. Sci. USA,  2008, 105(35), 12763-12768.
[http://dx.doi.org/10.1073/pnas.0806627105] [PMID: 18725631] 
[191] 
Günther, S.; von Eichborn, J.; May, P.; Preissner, R. JAIL: a structure-based interface library for macromolecules. Nucleic Acids Res.,  2009, 37(Database issue), D338-D341.
[http://dx.doi.org/10.1093/nar/gkn599] [PMID: 18832369] 
[192] 
Pieper, U.; Webb, B.M.; Barkan, D.T.; Schneidman-Duhovny, D.; Schlessinger, A.; Braberg, H.; Yang, Z.; Meng, E.C.; Pettersen, E.F.; Huang, C.C.; Datta, R.S.; Sampathkumar, P.; Madhusudhan, M.S.; Sjölander, K.; Ferrin, T.E.; Burley, S.K.; Sali, A. ModBase, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res.,  2011, 39(Database issue), D465-D474.
[http://dx.doi.org/10.1093/nar/gkq1091] [PMID: 21097780] 
[193] 
Blohm, P.; Frishman, G.; Smialowski, P.; Goebels, F.; Wachinger, B.; Ruepp, A.; Frishman, D. Negatome 2.0: a database of non-interacting proteins derived by literature mining, manual annotation and protein structure analysis. Nucleic Acids Res.,  2014, 42(Database issue), D396-D400.
[http://dx.doi.org/10.1093/nar/gkt1079] [PMID: 24214996] 
[194] 
Smialowski, P.; Pagel, P.; Wong, P.; Brauner, B.; Dunger, I.; Fobo, G.; Frishman, G.; Montrone, C.; Rattei, T.; Frishman, D.; Ruepp, A. The Negatome database: a reference set of non-interacting protein pairs. Nucleic Acids Res.,  2010, 38(Database issue), D540-D544.
[http://dx.doi.org/10.1093/nar/gkp1026] [PMID: 19920129] 
[195] 
Hamosh, A.; Scott, A.F.; Amberger, J.S.; Bocchini, C.A.; McKusick, V.A. Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res.,  2005, 33(Database issue), D514-D517.
[http://dx.doi.org/10.1093/nar/gki033] [PMID: 15608251] 
[196] 
Scott, M.S.; Barton, G.J. Probabilistic prediction and ranking of human protein-protein interactions. BMC Bioinformatics,  2007, 8, 239.
[http://dx.doi.org/10.1186/1471-2105-8-239] 
[197] 
McDowall, M.D.; Scott, M.S.; Barton, G.J. PIPs: human protein-protein interaction prediction database. Nucleic Acids Res.,  2009, 37(Database issue), D651-D656.
[http://dx.doi.org/10.1093/nar/gkn870] [PMID: 18988626] 
[198] 
Zhang, Q.C.; Petrey, D.; Garzón, J.I.; Deng, L.; Honig, B. PrePPI: a structure-informed database of protein-protein interactions. Nucleic Acids Res.,  2013, 41(Database issue), D828-D833.
[PMID: 23193263] 
[199] 
Chandonia, J.M.; Fox, N.K.; Brenner, S.E. SCOPe: classification of large macromolecular structures in the structural classification of proteins-extended database. Nucleic Acids Res.,  2019, 47(D1), D475-D481.
[http://dx.doi.org/10.1093/nar/gky1134] [PMID: 30500919] 
[200] 
Bienert, S.; Waterhouse, A.; de Beer, T.A.; Tauriello, G.; Studer, G.; Bordoli, L.; Schwede, T. The SWISS-MODEL Repository-new features and functionality. Nucleic Acids Res.,  2017, 45(D1), D313-D319.
[http://dx.doi.org/10.1093/nar/gkw1132] [PMID: 27899672] 
[201] 
Szklarczyk, D.; Gable, A.L.; Lyon, D.; Junge, A.; Wyder, S.; Huerta-Cepas, J.; Simonovic, M.; Doncheva, N.T.; Morris, J.H.; Bork, P.; Jensen, L.J.; Mering, C.V. STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res.,  2019, 47(D1), D607-D613.
[http://dx.doi.org/10.1093/nar/gky1131] [PMID: 30476243] 
[202] 
Basse, M.J.; Betzi, S.; Morelli, X.; Roche, P. 2P2Idb v2: update of a structural database dedicated to orthosteric modulation of protein-protein interactions. Database (Oxford),  2016, 2016, baw007
[203] 
Morelli, X.; Bourgeas, R.; Roche, P. Chemical and structural lessons from recent successes in protein-protein interaction inhibition (2P2I). Curr. Opin. Chem. Biol.,  2011, 15(4), 475-481.
[http://dx.doi.org/10.1016/j.cbpa.2011.05.024] [PMID: 21684802] 
[204] 
Labbé, C.M.; Laconde, G.; Kuenemann, M.A.; Villoutreix, B.O.; Sperandio, O. iPPI-DB: a manually curated and interactive database of small non-peptide inhibitors of protein-protein interactions. Drug Discov. Today,  2013, 18(19-20), 958-968.
[http://dx.doi.org/10.1016/j.drudis.2013.05.003] [PMID: 23688585] 
[205] 
Li, L.; Guo, D.; Huang, Y.; Liu, S.; Xiao, Y. ASPDock: protein-protein docking algorithm using atomic solvation parameters model. BMC Bioinformatics,  2011, 12(36)
[206] 
de Vries, S.J.; Schindler, C.E.; Chauvot de Beauchêne, I.; Zacharias, M. A web interface for easy flexible protein-protein docking with ATTRACT. Biophys. J.,  2015, 108(3), 462-465.
[http://dx.doi.org/10.1016/j.bpj.2014.12.015] [PMID: 25650913] 
[207] 
Huang, B.; Schroeder, M. Using protein binding site prediction to improve protein docking. Gene,  2008, 422(8)
[http://dx.doi.org/10.1016/j.gene.2008.06.014] 
[208] 
Pons, C.; Jiménez-González, D.; González-Álvarez, C.; Servat, H.; Cabrera-Benítez, D.; Aguilar, X.; Fernández-Recio, J. Cell-Dock: high-performance protein-protein docking. Bioinformatics,  2012, 28(18), 2394-2396.
[http://dx.doi.org/10.1093/bioinformatics/bts454] [PMID: 22815362] 
[209] 
Inbar, Y.; Benyamini, H.; Nussinov, R.; Wolfson, H.J. Combinatorial docking approach for structure prediction of large proteins and multi-molecular assemblies. Phys. Biol.,  2005, 2(4), S156-S165.
[http://dx.doi.org/10.1088/1478-3975/2/4/S10] [PMID: 16280621] 
[210] 
Viswanath, S.; Ravikant, D.V.; Elber, R. Dock/pierr: web server for structure prediction of protein-protein complexes. Methods Mol. Biol.,  2014, 1137, 199-207.
[211] 
Roberts, V.A.; Thompson, E.E.; Pique, M.E.; Perez, M.S.; Ten Eyck, L.F. DOT2: Macromolecular docking with improved biophysical models. J. Comput. Chem.,  2013, 34(20), 1743-1758.
[http://dx.doi.org/10.1002/jcc.23304] [PMID: 23695987] 
[212] 
Bajaj, C.; Chowdhury, R.; Siddavanahalli, V. F2Dock: fast Fourier protein-protein docking. IEEE/ACM Trans. Comput. Biol. Bioinformatics,  2011, 8(1), 45-58.
[http://dx.doi.org/10.1109/TCBB.2009.57] [PMID: 21071796] 
[213] 
Schneidman-Duhovny, D.; Hammel, M.; Tainer, J.A.; Sali, A. FoXS, FoXSDock and MultiFoXS: Single-state and multi-state structural modeling of proteins and their complexes based on SAXS profiles. Nucleic Acids Res.,  2016, 44(W1), W424-429.
[http://dx.doi.org/10.1093/nar/gkw389] [PMID: 27151198] 
[214] 
Ramírez-Aportela, E.; López-Blanco, J.R.; Chacón, P. FRODOCK 2.0: fast protein-protein docking server. Bioinformatics,  2016, 32(15), 2386-2388.
[http://dx.doi.org/10.1093/bioinformatics/btw141] [PMID: 27153583] 
[215] 
Tovchigrechko, A; Vakser, IA IA Gramm-x public web server for protein-protein docking.  Nucleic Acids Res,  2006, 34(Web Server
 issue), W310-314.
[http://dx.doi.org/10.1093/nar/gkl206] 
[216] 
Dominguez, C.; Boelens, R.; Bonvin, A.M. HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. J. Am. Chem. Soc.,  2003, 125(7), 1731-1737.
[http://dx.doi.org/10.1021/ja026939x] [PMID: 12580598] 
[217] 
Yan, Y.; Zhang, D.; Zhou, P.; Li, B.; Huang, S.Y. HDOCK: a web server for protein-protein and protein-DNA/RNA docking based on a hybrid strategy. Nucleic Acids Res.,  2017, 45(W1), W365-W373.
[http://dx.doi.org/10.1093/nar/gkx407] [PMID: 28521030] 
[218] 
Ritchie, D.W.; Venkatraman, V. Ultra-fast FFT protein docking on graphics processors. Bioinformatics,  2010, 26(19), 2398-2405.
[http://dx.doi.org/10.1093/bioinformatics/btq444] [PMID: 20685958] 
[219] 
Fernández-Recio, J.; Totrov, M.; Abagyan, R. ICM-DISCO docking by global energy optimization with fully flexible side-chains. Proteins,  2003, 52(1), 113-117.
[http://dx.doi.org/10.1002/prot.10383] [PMID: 12784376] 
[220] 
Méndez, R.; Leplae, R.; Lensink, M.F.; Wodak, S.J. Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures. Proteins,  2005, 60(2), 150-169.
[http://dx.doi.org/10.1002/prot.20551] [PMID: 15981261] 
[221] 
Méndez, R.; Leplae, R.; De Maria, L.; Wodak, S.J. Assessment of blind predictions of protein-protein interactions: current status of docking methods. Proteins,  2003, 52(1), 51-67.
[http://dx.doi.org/10.1002/prot.10393] [PMID: 12784368] 
[222] 
Jiménez-García, B.; Roel-Touris, J.; Romero-Durana, M.; Vidal, M.; Jiménez-González, D.; Fernández-Recio, J. LightDock: a new multi-scale approach to protein-protein docking. Bioinformatics,  2018, 34(1), 49-55.
[http://dx.doi.org/10.1093/bioinformatics/btx555] [PMID: 28968719] 
[223] 
Huang, S.Y.; Zou, X. MDockPP: A hierarchical approach for protein-protein docking and its application to CAPRI rounds 15-19. Proteins,  2010, 78(15), 3096-3103.
[http://dx.doi.org/10.1002/prot.22797] [PMID: 20635420] 
[224] 
Ohue, M.; Matsuzaki, Y.; Uchikoga, N.; Ishida, T.; Akiyama, Y. MEGADOCK: an all-to-all protein-protein interaction prediction system using tertiary structure data. Protein Pept. Lett.,  2014, 21(8), 766-778.
[http://dx.doi.org/10.2174/09298665113209990050] [PMID: 23855673] 
[225] 
Ohue, M.; Shimoda, T.; Suzuki, S.; Matsuzaki, Y.; Ishida, T.; Akiyama, Y. MEGADOCK 4.0: an ultra-high-performance protein-protein docking software for heterogeneous supercomputers. Bioinformatics,  2014, 30(22), 3281-3283.
[http://dx.doi.org/10.1093/bioinformatics/btu532] [PMID: 25100686] 
[226] 
Schneidman-Duhovny, D; Inbar, Y; Nussinov, R; Wolfson, HJ Patchdock and symmdock: Servers for rigid and symmetric
 docking. Nucleic Acids Res,  2005, 33(Web Server issue), W363-367.
[227] 
Jiménez-García, B.; Pons, C.; Fernández-Recio, J. pyDockWEB: a web server for rigid-body protein-protein docking using electrostatics and desolvation scoring. Bioinformatics,  2013, 29(13), 1698-1699.
[http://dx.doi.org/10.1093/bioinformatics/btt262] [PMID: 23661696] 
[228] 
Lyskov, S; Gray, JJ The rosettadock server for local protein-protein docking. Nucleic Acids Res,  2008, 36(Web Server issue), W233-238.
[http://dx.doi.org/10.1093/nar/gkn216] 
[229] 
Terashi, G.; Takeda-Shitaka, M.; Kanou, K.; Iwadate, M.; Takaya, D.; Umeyama, H. The SKE-DOCK server and human teams based on a combined method of shape complementarity and free energy estimation. Proteins,  2007, 69(4), 866-872.
[http://dx.doi.org/10.1002/prot.21772] [PMID: 17853449] 
[230] 
Torchala, M.; Moal, I.H.; Chaleil, R.A.; Fernandez-Recio, J.; Bates, P.A. SwarmDock: a server for flexible protein-protein docking. Bioinformatics,  2013, 29(6), 807-809.
[http://dx.doi.org/10.1093/bioinformatics/btt038] [PMID: 23343604] 
[231] 
Venkatraman, V.; Sael, L.; Kihara, D. Potential for protein surface shape analysis using spherical harmonics and 3D Zernike descriptors. Cell Biochem. Biophys.,  2009, 54(1-3), 23-32.
[http://dx.doi.org/10.1007/s12013-009-9051-x] [PMID: 19521674] 
[232] 
Pierce, B.G.; Wiehe, K.; Hwang, H.; Kim, B.H.; Vreven, T.; Weng, Z. ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers. Bioinformatics,  2014, 30(12), 1771-1773.
[http://dx.doi.org/10.1093/bioinformatics/btu097] [PMID: 24532726] 
[233] 
Kozakov, D.; Hall, D.R.; Xia, B.; Porter, K.A.; Padhorny, D.; Yueh, C.; Beglov, D.; Vajda, S. The ClusPro web server for protein-protein docking. Nat. Protoc.,  2017, 12(2), 255-278.
[http://dx.doi.org/10.1038/nprot.2016.169] [PMID: 28079879] 
[234] 
Segura, J.; Marín-López, M.A.; Jones, P.F.; Oliva, B.; Fernandez-Fuentes, N. VORFFIP-driven dock: V-D2OCK, a fast and accurate protein docking strategy. PLoS One,  2015, 10(3), e0118107
[http://dx.doi.org/10.1371/journal.pone.0118107] [PMID: 25763838] 
[235] 
Bock, J.R.; Gough, D.A. Predicting protein--protein interactions from primary structure. Bioinformatics,  2001, 17(5), 455-460.
[http://dx.doi.org/10.1093/bioinformatics/17.5.455] [PMID: 11331240] 
[236] 
Chen, X.W.; Liu, M. Prediction of protein-protein interactions using random decision forest framework. Bioinformatics,  2005, 21(24), 4394-4400.
[http://dx.doi.org/10.1093/bioinformatics/bti721] [PMID: 16234318] 
[237] 
Mukherjee, S.; Zhang, Y. Protein-protein complex structure predictions by multimeric threading and template recombination. Structure,  2011, 19(7), 955-966.
[http://dx.doi.org/10.1016/j.str.2011.04.006] [PMID: 21742262] 
[238] 
Cheng, Y.; Oldfield, C.J.; Meng, J.; Romero, P.; Uversky, V.N.; Dunker, A.K. Mining alpha-helix-forming molecular recognition features with cross species sequence alignments. Biochemistry,  2007, 46(47), 13468-13477.
[http://dx.doi.org/10.1021/bi7012273] [PMID: 17973494] 
[239] 
Chen, H.; Zhou, H.X. Prediction of interface residues in protein-protein complexes by a consensus neural network method: test against NMR data. Proteins,  2005, 61(1), 21-35.
[http://dx.doi.org/10.1002/prot.20514] [PMID: 16080151] 
[240] 
Rawi, R.; Mall, R.; Kunji, K.; El Anbari, M.; Aupetit, M.; Ullah, E.; Bensmail, H. COUSCOus: improved protein contact prediction using an empirical Bayes covariance estimator. BMC Bioinformatics,  2016, 17(1), 533.
[http://dx.doi.org/10.1186/s12859-016-1400-3] [PMID: 27978812] 
[241] 
Gao, M.; Zhou, H.; Skolnick, J. DESTINI: A deep-learning approach to contact-driven protein structure prediction. Sci. Rep.,  2019, 9(1), 3514.
[http://dx.doi.org/10.1038/s41598-019-40314-1] [PMID: 30837676] 
[242] 
Lopez, G Valencia, A Tress ML Firestar--prediction of
 functionally important residues using structural templates and
 alignment reliability. Nucleic Acids Res,  2007, 35(Web Server issue), W573-577.
[243] 
Huang, Y.A.; You, Z.H.; Chen, X.; Yan, G.Y. Improved protein-protein interactions prediction via weighted sparse representation model combining continuous wavelet descriptor and PseAA composition. BMC Syst. Biol.,  2016, 10(Suppl. 4), 120.
[http://dx.doi.org/10.1186/s12918-016-0360-6] [PMID: 28155718] 
[244] 
Negi, S.S.; Schein, C.H.; Oezguen, N.; Power, T.D.; Braun, W. InterProSurf: a web server for predicting interacting sites on protein surfaces. Bioinformatics,  2007, 23(24), 3397-3399.
[http://dx.doi.org/10.1093/bioinformatics/btm474] [PMID: 17933856] 
[245] 
Olmea, O.; Rost, B.; Valencia, A. Effective use of sequence correlation and conservation in fold recognition. J. Mol. Biol.,  1999, 293(5), 1221-1239.
[http://dx.doi.org/10.1006/jmbi.1999.3208] [PMID: 10547297] 
[246] 
Simonetti, FL; Teppa, E Chernomoretz, A Nielsen M Marino
 Buslje C. Mistic: Mutual information server to infer coevolution. Nucleic Acids Res,  2013, 41(Web Server issue), W8-14.
[247] 
Kufareva, I.; Budagyan, L.; Raush, E.; Totrov, M.; Abagyan, R. PIER: protein interface recognition for structural proteomics. Proteins,  2007, 67(2), 400-417.
[http://dx.doi.org/10.1002/prot.21233] [PMID: 17299750] 
[248] 
Liang, S.; Zhang, C.; Liu, S.; Zhou, Y. Protein binding site prediction using an empirical scoring function. Nucleic Acids Res.,  2006, 34(13), 3698-3707.
[http://dx.doi.org/10.1093/nar/gkl454] [PMID: 16893954] 
[249] 
Chatterjee, P.; Basu, S.; Kundu, M.; Nasipuri, M.; Plewczynski, D. PPI_SVM: prediction of protein-protein interactions using machine learning, domain-domain affinities and frequency tables. Cell. Mol. Biol. Lett.,  2011, 16(2), 264-278.
[http://dx.doi.org/10.2478/s11658-011-0008-x] [PMID: 21442443] 
[250] 
Guo, Y.; Li, M.; Pu, X.; Li, G.; Guang, X.; Xiong, W.; Li, J. PRED_PPI: a server for predicting protein-protein interactions based on sequence data with probability assignment. BMC Res. Notes,  2010, 3(145)
[251] 
Kuo, T.H.; Li, K.B. Predicting protein-protein interaction sites using sequence descriptors and site propensity of neighboring amino acids. Int. J. Mol. Sci.,  2016, 17(11), E1788
[http://dx.doi.org/10.3390/ijms17111788] [PMID: 27792167] 
[252] 
Murakami, Y.; Mizuguchi, K. Applying the Naïve Bayes classifier with kernel density estimation to the prediction of protein-protein interaction sites. Bioinformatics,  2010, 26(15), 1841-1848.
[http://dx.doi.org/10.1093/bioinformatics/btq302] [PMID: 20529890] 
[253] 
Valdar, W.S. Scoring residue conservation. Proteins,  2002, 48(2), 227-241.
[http://dx.doi.org/10.1002/prot.10146] [PMID: 12112692] 
[254] 
Shulman-Peleg, A.; Nussinov, R.; Wolfson, H.J. Recognition of functional sites in protein structures. J. Mol. Biol.,  2004, 339(3), 607-633.
[http://dx.doi.org/10.1016/j.jmb.2004.04.012] [PMID: 15147845] 
[255] 
Wang, B.; Chen, P.; Huang, D.S.; Li, J.J.; Lok, T.M.; Lyu, M.R. Predicting protein interaction sites from residue spatial sequence profile and evolution rate. FEBS Lett.,  2006, 580(2), 380-384.
[http://dx.doi.org/10.1016/j.febslet.2005.11.081] [PMID: 16376878] 
[256] 
de Vries, S.J.; van Dijk, A.D.; Bonvin, A.M. WHISCY: what information does surface conservation yield? Application to data-driven docking. Proteins,  2006, 63(3), 479-489.
[http://dx.doi.org/10.1002/prot.20842] [PMID: 16450362] 
[257] 
de Vries, S.J.; Bonvin, A.M. CPORT: a consensus interface predictor and its performance in prediction-driven docking with HADDOCK. PLoS One,  2011, 6(3), e17695
[http://dx.doi.org/10.1371/journal.pone.0017695] [PMID: 21464987] 
[258] 
Qin, S.; Zhou, H.X. meta-PPISP: a meta web server for protein-protein interaction site prediction. Bioinformatics,  2007, 23(24), 3386-3387.
[http://dx.doi.org/10.1093/bioinformatics/btm434] [PMID: 17895276] 
[259] 
Tjong, H; Qin, S; Zhou, HX Pi2pe: Protein interface/interior
 prediction engine. Nucleic Acids Res,  2007, 35(Web Server issue), W357-362.
[260] 
Sael, L.; Li, B.; La, D.; Fang, Y.; Ramani, K.; Rustamov, R.; Kihara, D. Fast protein tertiary structure retrieval based on global surface shape similarity. Proteins,  2008, 72(4), 1259-1273.
[http://dx.doi.org/10.1002/prot.22030] [PMID: 18361455] 
[261] 
Pei, J.; Grishin, N.V. AL2CO: calculation of positional conservation in a protein sequence alignment. Bioinformatics,  2001, 17(8), 700-712.
[http://dx.doi.org/10.1093/bioinformatics/17.8.700] [PMID: 11524371] 
[262] 
Palma, P.N.; Krippahl, L.; Wampler, J.E.; Moura, J.J. BiGGER: a new (soft) docking algorithm for predicting protein interactions. Proteins,  2000, 39(4), 372-384.
[http://dx.doi.org/10.1002/(SICI)1097-0134(20000601)39:4<372:AID-PROT100>3.0.CO;2-Q] [PMID: 10813819] 
[263] 
Powers, R.; Copeland, J.C.; Stark, J.L.; Caprez, A.; Guru, A.; Swanson, D. Searching the protein structure database for ligand-binding site similarities using CPASS v.2. BMC Res. Notes,  2011, 4(17)
[264] 
Bernauer, J.; Bahadur, R.P.; Rodier, F.; Janin, J.; Poupon, A. DiMoVo: a Voronoi tessellation-based method for discriminating crystallographic and biological protein-protein interactions. Bioinformatics,  2008, 24(5), 652-658.
[http://dx.doi.org/10.1093/bioinformatics/btn022] [PMID: 18204058] 
[265] 
Hamer, R.; Luo, Q.; Armitage, J.P.; Reinert, G.; Deane, C.M. i-Patch: interprotein contact prediction using local network information. Proteins,  2010, 78(13), 2781-2797.
[http://dx.doi.org/10.1002/prot.22792] [PMID: 20635422] 
[266] 
Jia, J.; Li, X.; Qiu, W.; Xiao, X.; Chou, K.C. C Ippi-pseaac(cgr): Identify protein-protein interactions by incorporating chaos game representation into PseAAC. J. Theor. Biol.,  2019, 460, 195-203.
[267] 
Xue, L.C.; Dobbs, D.; Honavar, V. HomPPI: a class of sequence homology based protein-protein interface prediction methods. BMC Bioinformatics,  2011, 12(244)
[268] 
Lu, L.; Lu, H.; Skolnick, J. MULTIPROSPECTOR: an algorithm for the prediction of protein-protein interactions by multimeric threading. Proteins,  2002, 49(3), 350-364.
[http://dx.doi.org/10.1002/prot.10222] [PMID: 12360525] 
[269] 
Chen, H.; Skolnick, J. M-TASSER: an algorithm for protein quaternary structure prediction. Biophys. J.,  2008, 94(3), 918-928.
[http://dx.doi.org/10.1529/biophysj.107.114280] [PMID: 17905848] 
[270] 
Ponstingl, H.; Kabir, T.; Thornton, J.M. Automatic inference of protein quaternary structure from crystals. J. Appl. Cryst.,  2003, 36(7)
[http://dx.doi.org/10.1107/S0021889803012421] 
[271] 
Henrick, K.; Thornton, J.M. PQS: a protein quaternary structure file server. Trends Biochem. Sci.,  1998, 23(9), 358-361.
[http://dx.doi.org/10.1016/S0968-0004(98)01253-5] [PMID: 9787643] 
[272] 
Rashid, M.; Ramasamy, S.; Raghava, G.P. A simple approach for predicting protein-protein interactions. Curr. Protein Pept. Sci.,  2010, 11(7), 589-600.
[http://dx.doi.org/10.2174/138920310794109120] [PMID: 20887258] 
[273] 
Lua, R.C.; Lichtarge, O. PyETV: a PyMOL evolutionary trace viewer to analyze functional site predictions in protein complexes. Bioinformatics,  2010, 26(23), 2981-2982.
[http://dx.doi.org/10.1093/bioinformatics/btq566] [PMID: 20929911] 
[274] 
Milburn, D.; Laskowski, R.A.; Thornton, J.M. Sequences annotated by structure: a tool to facilitate the use of structural information in sequence analysis. Protein Eng.,  1998, 11(10), 855-859.
[http://dx.doi.org/10.1093/protein/11.10.855] [PMID: 9862203] 
[275] 
Meireles, LM; Domling, AS; Camacho, CJ Anchor: A web server and database for analysis of protein-protein interaction binding pockets for drug discovery. Nucleic Acids Res,  2010, 38(Web
 Server issue), W407-411.
[276] 
Bradford, J.R.; Needham, C.J.; Bulpitt, A.J.; Westhead, D.R. Insights into protein-protein interfaces using a Bayesian network prediction method. J. Mol. Biol.,  2006, 362(2), 365-386.
[http://dx.doi.org/10.1016/j.jmb.2006.07.028] [PMID: 16919296] 
[277] 
Shingate, P.; Manoharan, M.; Sukhwal, A.; Sowdhamini, R. ECMIS: computational approach for the identification of hotspots at protein-protein interfaces. BMC Bioinformatics,  2014, 15(303)
[278] 
Guerois, R.; Nielsen, J.E.; Serrano, L. Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. J. Mol. Biol.,  2002, 320(2), 369-387.
[http://dx.doi.org/10.1016/S0022-2836(02)00442-4] [PMID: 12079393] 
[279] 
Xia, J.; Yue, Z.; Di, Y.; Zhu, X.; Zheng, C.H. Predicting hot spots in protein interfaces based on protrusion index, pseudo hydrophobicity and electron-ion interaction pseudopotential features. Oncotarget,  2016, 7(14), 18065-18075.
[http://dx.doi.org/10.18632/oncotarget.7695] [PMID: 26934646] 
[280] 
Sumbalova, L.; Stourac, J.; Martinek, T.; Bednar, D.; Damborsky, J. HotSpot Wizard 3.0: web server for automated design of mutations and smart libraries based on sequence input information. Nucleic Acids Res.,  2018, 46(W1), W356-W362.
[http://dx.doi.org/10.1093/nar/gky417] [PMID: 29796670] 
[281] 
Darnell, S.J.; Page, D.; Mitchell, J.C. An automated decision-tree approach to predicting protein interaction hot spots. Proteins,  2007, 68(4), 813-823.
[http://dx.doi.org/10.1002/prot.21474] [PMID: 17554779] 
[282] 
Sukhwal, A.; Sowdhamini, R. Ppcheck: A webserver for the quantitative analysis of protein-protein interfaces and prediction of residue hotspots. Bioinform. Biol. Insights,  2015, 9, 141-151.
[283] 
Munteanu, C.R.; Pimenta, A.C.; Fernandez-Lozano, C.; Melo, A.; Cordeiro, M.N.; Moreira, I.S. Solvent accessible surface area-based hot-spot detection methods for protein-protein and protein-nucleic acid interfaces. J. Chem. Inf. Model.,  2015, 55(5), 1077-1086.
[http://dx.doi.org/10.1021/ci500760m] [PMID: 25845030] 
[284] 
Deng, L.; Guan, J.H.; Dong, Q.W.; Zhou, S.G. SemiHS: an iterative semi-supervised approach for predicting protein-protein interaction hot spots. Protein Pept. Lett.,  2011, 18(9), 896-905.
[http://dx.doi.org/10.2174/092986611796011419] [PMID: 21529341] 
[285] 
Moreira, I.S.; Koukos, P.I.; Melo, R.; Almeida, J.G.; Preto, A.J.; Schaarschmidt, J.; Trellet, M.; Gümüş, Z.H.; Costa, J.; Bonvin, A.M.J.J. Spoton: High accuracy identification of protein-protein interface hot-spots. Sci. Rep.,  2017, 7(1), 8007.
[http://dx.doi.org/10.1038/s41598-017-08321-2] [PMID: 28808256] 
[286] 
Wang, L.; Liu, Z.P.; Zhang, X.S.; Chen, L. Prediction of hot spots in protein interfaces using a random forest model with hybrid features. Protein Eng. Des. Sel.,  2012, 25(3), 119-126.
[http://dx.doi.org/10.1093/protein/gzr066] [PMID: 22258275] 
[287] 
Ye, L; Kuang, Q; Jiang, L; Luo, J; Jiang, Y; Ding, Z; Li, Y.; Li, M. Prediction of hot spots residues in protein–protein interface using network feature and microenvironment feature.  Chemom Intell Lab Syst,,  2014, 131(15 Feb), 16-21.
[288] 
Thorn, K.S.; Bogan, A.A. ASEdb: a database of alanine mutations and their effects on the free energy of binding in protein interactions. Bioinformatics,  2001, 17(3), 284-285.
[http://dx.doi.org/10.1093/bioinformatics/17.3.284] [PMID: 11294795] 
[289] 
Liu, Q.; Chen, P.; Wang, B.; Zhang, J.; Li, J. dbMPIKT: a database of kinetic and thermodynamic mutant protein interactions. BMC Bioinformatics,  2018, 19(1), 455.
[http://dx.doi.org/10.1186/s12859-018-2493-7] [PMID: 30482172] 
[290] 
Segura, J.; Fernandez-Fuentes, N. PCRPi-DB: a database of computationally annotated hot spots in protein interfaces. Nucleic Acids Res.,  2011, 39(Database issue), D755-D760.
[http://dx.doi.org/10.1093/nar/gkq1068] [PMID: 21097468] 
[291] 
Kumar, M.D.; Gromiha, M.M. Pint: Protein-protein interactions thermodynamic database. Nucleic Acids Res.,  2006, 34(Database issue), D195-D198.
[http://dx.doi.org/10.1093/nar/gkj017] [PMID: 16381844] 
[292] 
Jemimah, S.; Yugandhar, K.; Michael Gromiha, M. PROXiMATE: a database of mutant protein-protein complex thermodynamics and kinetics. Bioinformatics,  2017, 33(17), 2787-2788.
[http://dx.doi.org/10.1093/bioinformatics/btx312] [PMID: 28498885] 
[293] 
Jankauskaite, J.; Jiménez-García, B.; Dapkunas, J.; Fernández-Recio, J.; Moal, I.H. SKEMPI 2.0: an updated benchmark of changes in protein-protein binding energy, kinetics and thermodynamics upon mutation. Bioinformatics,  2019, 35(3), 462-469.
[http://dx.doi.org/10.1093/bioinformatics/bty635] [PMID: 30020414] 
Cite As
Current Topics in Medicinal Chemistry

Decoding Protein-protein Interactions: An Overview

Abstract

Graphical Abstract
