Login Register Cart 0
Review Article

蛋白质-蛋白质相互作用的映射：揭示相互作用组的基于Web的资源

卷 26, 期 21, 2019

页: [3890 - 3910] 页: 21

弟呕挨: 10.2174/0929867325666180214113704

价格: $65

摘要

背景：通过利用测序，晶体学，光谱学和二杂交筛选领域的伴随进展而发现的大量蛋白质-蛋白质相互作用（PPI），提示了重塑药物发现的惊人前景。 PPI空间包括多达650 000个实体，是每种人类疾病潜在治疗目标的非凡储备。为了使现代药物发现计划能够利用这一点，我们应该能够辨别与特定疾病和相应的正常生理相关的完整PPI图。目标：在这里，我们将回顾社区可用的用于预测PPI的计算程序以及用于存储实验注释的交互的基于Web的资源。 方法：我们比较了预测工具：iLoops，Struck2Net，HOMCOS，COTH，PrePPI，InterPreTS和PRISM的能力，以预测最近发现的蛋白质相互作用。 结果：我们描述了基于序列和基于结构的PPI预测工具并解决了它们的特殊性。此外，由于预测算法的实用性在很大程度上取决于所建立实验数据的质量和数量；因此，我们广泛讨论了蛋白质相互作用的社区资源。我们关注的是活跃的和最近更新的主要和次要PPI数据库，专门针对主题或物种的存储库以及包括实验性PPI和预测性PPI的数据库。 结论：PPI复合物是重要生理过程的基础，因此是细胞穿透配体的可能靶标。可靠的计算PPI预测可以通过为实验研究确定治疗相关的蛋白质-蛋白质复合物的优先级来加快新的靶标发现。

关键词: 蛋白质-蛋白质相互作用，计算预测，预测性能，高通量实验技术，相互作用组数据集，数据库。

« Previous Next »
[1]
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]
[2]
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]
[3]
Drew, K.; Lee, C.; Huizar, R.L.; Tu, F.; Borgeson, B.; McWhite, C.D.; Ma, Y.; Wallingford, J.B.; Marcotte, E.M. Integration of over 9,000 mass spectrometry experiments builds a global map of human protein complexes. Mol. Syst. Biol., 2017, 13(6), 932.
[http://dx.doi.org/10.15252/msb.20167490] [PMID: 28596423]
[4]
Hopkins, A.L.; Groom, C.R. The druggable genome. Nat. Rev. Drug Discov., 2002, 1(9), 727-730.
[http://dx.doi.org/10.1038/nrd892] [PMID: 12209152]
[5]
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]
[6]
Petta, I.; Lievens, S.; Libert, C.; Tavernier, J.; De Bosscher, K. Modulation of protein-protein interactions for the development of novel therapeutics. Mol. Ther., 2016, 24(4), 707-718.
[http://dx.doi.org/10.1038/mt.2015.214] [PMID: 26675501]
[7]
Zarzycka, B.; Kuenemann, M.A.; Miteva, M.A.; Nicolaes, G.A.F.; Vriend, G.; Sperandio, O. Stabilization of protein-protein interaction complexes through small molecules. Drug Discov. Today, 2016, 21(1), 48-57.
[http://dx.doi.org/10.1016/j.drudis.2015.09.011] [PMID: 26434617]
[8]
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]
[9]
Nero, T.L.; Morton, C.J.; Holien, J.K.; Wielens, J.; Parker, M.W. Oncogenic protein interfaces: Small molecules, big challenges. Nat. Rev. Cancer, 2014, 14(4), 248-262.
[http://dx.doi.org/10.1038/nrc3690] [PMID: 24622521]
[10]
Andreeff, M.; Kelly, K.R.; Yee, K.; Assouline, S.; Strair, R.; Popplewell, L.; Bowen, D.; Martinelli, G.; Drummond, M.W.; Vyas, P.; Kirschbaum, M.; Iyer, S.P.; Ruvolo, V.; González, G.M.; Huang, X.; Chen, G.; Graves, B.; Blotner, S.; Bridge, P.; Jukofsky, L.; Middleton, S.; Reckner, M.; Rueger, R.; Zhi, J.; Nichols, G.; Kojima, K. Results of the Phase I Trial of RG7112, a Small-Molecule MDM2 Antagonist in Leukemia. Clin. Cancer Res., 2016, 22(4), 868-876.
[http://dx.doi.org/10.1158/1078-0432.CCR-15-0481] [PMID: 26459177]
[11]
Ding, Q.; Zhang, Z.; Liu, J.J.; Jiang, N.; Zhang, J.; Ross, T.M.; Chu, X.J.; Bartkovitz, D.; Podlaski, F.; Janson, C.; Tovar, C.; Filipovic, Z.M.; Higgins, B.; Glenn, K.; Packman, K.; Vassilev, L.T.; Graves, B. Discovery of RG7388, a potent and selective p53-MDM2 inhibitor in clinical development. J. Med. Chem., 2013, 56(14), 5979-5983.
[http://dx.doi.org/10.1021/jm400487c] [PMID: 23808545]
[12]
Wang, S.; Sun, W.; Zhao, Y.; McEachern, D.; Meaux, I.; Barrière, C.; Stuckey, J.A.; Meagher, J.L.; Bai, L.; Liu, L.; Hoffman-Luca, C.G.; Lu, J.; Shangary, S.; Yu, S.; Bernard, D.; Aguilar, A.; Dos-Santos, O.; Besret, L.; Guerif, S.; Pannier, P.; Gorge-Bernat, D.; Debussche, L. SAR405838: An optimized inhibitor of MDM2-p53 interaction that induces complete and durable tumor regression. Cancer Res., 2014, 74(20), 5855-5865.
[http://dx.doi.org/10.1158/0008-5472.CAN-14-0799] [PMID: 25145672]
[13]
Burgess, A.; Chia, K.M.; Haupt, S.; Thomas, D.; Haupt, Y.; Lim, E. Clinical Overview of MDM2/X-Targeted Therapies. Front. Oncol., 2016, 6, 7.
[http://dx.doi.org/10.3389/fonc.2016.00007] [PMID: 26858935]
[14]
Levin, N.M.B.; Pintro, V.O.; de Avila, M.B.; de Mattos, B.B.; De Azevedo, W.F. Jr Understanding the Structural Basis for Inhibition of Cyclin-Dependent Kinases. New Pieces in the Molecular Puzzle. Curr. Drug Targets, 2017, 18(9), 1104-1111.
[http://dx.doi.org/10.2174/1389450118666161116130155] [PMID: 27848884]
[15]
Kontopidis, G.; Andrews, M.J.; McInnes, C.; Plater, A.; Innes, L.; Renachowski, S.; Cowan, A.; Fischer, P.M. Truncation and optimisation of peptide inhibitors of cyclin-dependent kinase 2-cyclin a through structure-guided design. ChemMedChem, 2009, 4(7), 1120-1128.
[http://dx.doi.org/10.1002/cmdc.200900093] [PMID: 19472269]
[16]
Premnath, P.N.; Liu, S.; Perkins, T.; Abbott, J.; Anderson, E.; McInnes, C. Fragment based discovery of arginine isosteres through REPLACE: Towards non-ATP competitive CDK inhibitors. Bioorg. Med. Chem., 2014, 22(1), 616-622.
[http://dx.doi.org/10.1016/j.bmc.2013.10.039] [PMID: 24286762]
[17]
Nandha Premnath, P.; Craig, S.; McInnes, C. Development of inhibitors of protein-protein interactions through replace: Application to the design and development non-ATP competitive CDK inhibitors. J. Vis. Exp., 2015, 105(105)e52441
[http://dx.doi.org/10.3791/52441] [PMID: 26554946]
[18]
Premnath, P.N.; Craig, S.N.; Liu, S.; McInnes, C. Benzamide capped peptidomimetics as non-ATP competitive inhibitors of CDK2 using the REPLACE strategy. Bioorg. Med. Chem. Lett., 2016, 26(15), 3754-3760.
[http://dx.doi.org/10.1016/j.bmcl.2016.05.067] [PMID: 27297568]
[19]
de Azevedo, W.F. Opinion paper: Targeting multiple cyclin-dependent kinases (CDKs): A new strategy for molecular docking studies. Curr. Drug Targets, 2016, 17(1), 2.
[http://dx.doi.org/10.2174/138945011701151217100907] [PMID: 26687602]
[20]
Christ, F.; Voet, A.; Marchand, A.; Nicolet, S.; Desimmie, B.A.; Marchand, D.; Bardiot, D.; Van der Veken, N.J.; Van Remoortel, B.; Strelkov, S.V.; De Maeyer, M.; Chaltin, P.; Debyser, Z. Rational design of small-molecule inhibitors of the LEDGF/p75-integrase interaction and HIV replication. Nat. Chem. Biol., 2010, 6(6), 442-448.
[http://dx.doi.org/10.1038/nchembio.370] [PMID: 20473303]
[21]
Wang, Y.; Coulombe, R.; Cameron, D.R.; Thauvette, L.; Massariol, M.J.; Amon, L.M.; Fink, D.; Titolo, S.; Welchner, E.; Yoakim, C.; Archambault, J.; White, P.W. Crystal structure of the E2 transactivation domain of human papillomavirus type 11 bound to a protein interaction inhibitor. J. Biol. Chem., 2004, 279(8), 6976-6985.
[http://dx.doi.org/10.1074/jbc.M311376200] [PMID: 14634007]
[22]
Nooren, I.M.; Thornton, J.M. Diversity of protein-protein interactions. EMBO J., 2003, 22(14), 3486-3492.
[http://dx.doi.org/10.1093/emboj/cdg359] [PMID: 12853464]
[23]
Nooren, I.M.; Thornton, J.M. Structural characterisation and functional significance of transient protein-protein interactions. J. Mol. Biol., 2003, 325(5), 991-1018.
[http://dx.doi.org/10.1016/S0022-2836(02)01281-0] [PMID: 12527304]
[24]
Uversky, V.N. Intrinsic disorder-based protein interactions and their modulators. Curr. Pharm. Des., 2013, 19(23), 4191-4213.
[http://dx.doi.org/10.2174/1381612811319230005] [PMID: 23170892]
[25]
Zhang, Q.C.; Petrey, D.; Deng, L.; Qiang, L.; Shi, Y.; Thu, C.A.; Bisikirska, B.; Lefebvre, C.; Accili, D.; Hunter, T.; Maniatis, T.; Califano, A.; Honig, B. Structure-based prediction of protein-protein interactions on a genome-wide scale. Nature, 2012, 490(7421), 556-560.
[http://dx.doi.org/10.1038/nature11503] [PMID: 23023127]
[26]
Koh, G.C.; Porras, P.; Aranda, B.; Hermjakob, H.; Orchard, S.E. Analyzing protein-protein interaction networks. J. Proteome Res., 2012, 11(4), 2014-2031.
[http://dx.doi.org/10.1021/pr201211w] [PMID: 22385417]
[27]
Meysman, P.; Titeca, K.; Eyckerman, S.; Tavernier, J.; Goethals, B.; Martens, L.; Valkenborg, D.; Laukens, K. Protein complex analysis: From raw protein lists to protein interaction networks. Mass Spectrom. Rev., 2017, 36(5), 600-614.
[http://dx.doi.org/10.1002/mas.21485] [PMID: 26709718]
[28]
De Azevedo, W.F. Jr MolDock applied to structure-based virtual screening. Curr. Drug Targets, 2010, 11(3), 327-334.
[http://dx.doi.org/10.2174/138945010790711941] [PMID: 20210757]
[29]
Heberlé, G.; de Azevedo, W.F., Jr Bio-inspired algorithms applied to molecular docking simulations. Curr. Med. Chem., 2011, 18(9), 1339-1352.
[http://dx.doi.org/10.2174/092986711795029573] [PMID: 21366530]
[30]
Wass, M.N.; Fuentes, G.; Pons, C.; Pazos, F.; Valencia, A. Towards the prediction of protein interaction partners using physical docking. Mol. Syst. Biol., 2011, 7, 469.
[http://dx.doi.org/10.1038/msb.2011.3] [PMID: 21326236]
[31]
Kozakov, D.; Beglov, D.; Bohnuud, T.; Mottarella, S.E.; Xia, B.; Hall, D.R.; Vajda, S. How good is automated protein docking? Proteins, 2013, 81(12), 2159-2166.
[http://dx.doi.org/10.1002/prot.24403] [PMID: 23996272]
[32]
Vakser, I.A. Low-resolution structural modeling of protein interactome. Curr. Opin. Struct. Biol., 2013, 23(2), 198-205.
[http://dx.doi.org/10.1016/j.sbi.2012.12.003] [PMID: 23294579]
[33]
Xavier, M.M.; Heck, G.S.; Avila, M.B.; Levin, N.M.B.; Pintro, V.O.; Carvalho, N.L.; Azevedo, W.F. SAnDReS a computational tool for statistical analysis of docking results and development of scoring functions. Comb. Chem. High Throughput Screen., 2016, 19(10), 801-812.
[http://dx.doi.org/10.2174/1386207319666160927111347] [PMID: 27686428]
[34]
Zhang, Q.; Feng, T.; Xu, L.; Sun, H.; Pan, P.; Li, Y.; Li, D.; Hou, T. Recent advances in protein-protein docking. Curr. Drug Targets, 2016, 17(14), 1586-1594.
[http://dx.doi.org/10.2174/1389450117666160112112640] [PMID: 26758670]
[35]
Abdolmaleki, A.; Ghasemi, J.B.; Ghasemi, F. Computer aided drug design for multi-target drug design: SAR/QSAR, molecular docking and pharmacophore methods. Curr. Drug Targets, 2017, 18(5), 556-575.
[http://dx.doi.org/10.2174/1389450117666160101120822] [PMID: 26721410]
[36]
Scotti, L.; Mendonca, Junior F.J.; Ishiki, H.M.; Ribeiro, F.F.; Singla, R.K.; Barbosa Filho, J.M.; Da Silva, M.S.; Scotti, M.T. Docking Studies for Multi-Target Drugs. Curr. Drug Targets, 2017, 18(5), 592-604.
[http://dx.doi.org/10.2174/1389450116666150825111818] [PMID: 26302806]
[37]
Wodak, S.J.; Janin, J. Modeling protein assemblies: Critical Assessment of Predicted Interactions (CAPRI) 15 years hence.: 6TH CAPRI evaluation meeting April 17-19 Tel-Aviv, Israel. Proteins, 2017, 85(3), 357-358.
[http://dx.doi.org/10.1002/prot.25233] [PMID: 28019680]
[38]
Hamp, T.; Rost, B. More challenges for machine-learning protein interactions. Bioinformatics, 2015, 31(10), 1521-1525.
[http://dx.doi.org/10.1093/bioinformatics/btu857] [PMID: 25586513]
[39]
Park, Y.; Marcotte, E.M. Revisiting the negative example sampling problem for predicting protein-protein interactions. Bioinformatics, 2011, 27(21), 3024-3028.
[http://dx.doi.org/10.1093/bioinformatics/btr514] [PMID: 21908540]
[40]
Ben-Hur, A.; Noble, W.S. Choosing negative examples for the prediction of protein-protein interactions. BMC Bioinformatics, 2006, 7(Suppl. 1), S2.
[http://dx.doi.org/10.1186/1471-2105-7-S1-S2] [PMID: 16723005]
[41]
Martin, S.; Roe, D.; Faulon, J.L. Predicting protein-protein interactions using signature products. Bioinformatics, 2005, 21(2), 218-226.
[http://dx.doi.org/10.1093/bioinformatics/bth483] [PMID: 15319262]
[42]
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]
[43]
Planas-Iglesias, J.; Bonet, J.; García-García, J.; Marín-López, M.A.; Feliu, E.; Oliva, B. Understanding protein-protein interactions using local structural features. J. Mol. Biol., 2013, 425(7), 1210-1224.
[http://dx.doi.org/10.1016/j.jmb.2013.01.014] [PMID: 23353828]
[44]
Planas-Iglesias, J.; Marin-Lopez, M.A.; Bonet, J.; Garcia-Garcia, J.; Oliva, B. iLoops: A protein-protein interaction prediction server based on structural features. Bioinformatics, 2013, 29(18), 2360-2362.
[http://dx.doi.org/10.1093/bioinformatics/btt401] [PMID: 23842807]
[45]
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]
[46]
Perovic, V.; Sumonja, N.; Gemovic, B.; Toska, E.; Roberts, S.G.; Veljkovic, N. TRI_tool: A web-tool for prediction of protein-protein interactions in human transcriptional regulation. Bioinformatics, 2017, 33(2), 289-291.
[http://dx.doi.org/10.1093/bioinformatics/btw590] [PMID: 27605104]
[47]
Aloy, P.; Russell, R.B. InterPreTS: Protein interaction prediction through tertiary structure. Bioinformatics, 2003, 19(1), 161-162.
[http://dx.doi.org/10.1093/bioinformatics/19.1.161] [PMID: 12499311]
[48]
Fukuhara, N.; Kawabata, T. HOMCOS: A server to predict interacting protein pairs and interacting sites by homology modeling of complex structures. Nucleic Acids Res,, 2008, 36(Web Server issue), W185-W189.
[http://dx.doi.org/10.1093/nar/gkn218]
[49]
Fiser, A.; Sali, A. Modeller: Generation and refinement of homology-based protein structure models. Methods Enzymol., 2003, 374, 461-491.
[http://dx.doi.org/10.1016/S0076-6879(03)74020-8] [PMID: 14696385]
[50]
Lambert, C.; Léonard, N.; De Bolle, X.; Depiereux, E. ESyPred3D: Prediction of proteins 3D structures. Bioinformatics, 2002, 18(9), 1250-1256.
[http://dx.doi.org/10.1093/bioinformatics/18.9.1250] [PMID: 12217917]
[51]
Uchôa, H.B.; Jorge, G.E.; Freitas Da Silveira, N.J.; Camera, J.C., Jr; Canduri, F.; De Azevedo, W.F. Jr Parmodel: A web server for automated comparative modeling of proteins. Biochem. Biophys. Res. Commun., 2004, 325(4), 1481-1486.
[http://dx.doi.org/10.1016/j.bbrc.2004.10.192] [PMID: 15555595]
[52]
Kawabata, T. HOMCOS: An updated server to search and model complex 3D structures. J. Struct. Funct. Genomics, 2016, 17(4), 83-99.
[http://dx.doi.org/10.1007/s10969-016-9208-y] [PMID: 27522608]
[53]
Pulim, V.; Bienkowska, J.; Berger, B. LTHREADER: Prediction of extracellular ligand-receptor interactions in cytokines using localized threading. Protein Sci., 2008, 17(2), 279-292.
[http://dx.doi.org/10.1110/ps.073178108] [PMID: 18096641]
[54]
Bowie, J.U.; Lüthy, R.; Eisenberg, D. A method to identify protein sequences that fold into a known three-dimensional structure. Science, 1991, 253(5016), 164-170.
[http://dx.doi.org/10.1126/science.1853201] [PMID: 1853201]
[55]
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-W515.
[http://dx.doi.org/10.1093/nar/gkq481]
[56]
Hosur, R.; Peng, J.; Vinayagam, A.; Stelzl, U.; Xu, J.; Perrimon, N.; Bienkowska, J.; Berger, B. A computational framework for boosting confidence in high-throughput protein-protein interaction datasets. Genome Biol., 2012, 13(8), R76.
[http://dx.doi.org/10.1186/gb-2012-13-8-r76] [PMID: 22937800]
[57]
Hosur, R.; Xu, J.; Bienkowska, J.; Berger, B. iWRAP: An interface threading approach with application to prediction of cancer-related protein-protein interactions. J. Mol. Biol., 2011, 405(5), 1295-1310.
[http://dx.doi.org/10.1016/j.jmb.2010.11.025] [PMID: 21130772]
[58]
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]
[59]
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]
[60]
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]
[61]
Gao, M.; Skolnick, J. Structural space of protein-protein interfaces is degenerate, close to complete, and highly connected. Proc. Natl. Acad. Sci. USA, 2010, 107(52), 22517-22522.
[http://dx.doi.org/10.1073/pnas.1012820107] [PMID: 21149688]
[62]
Tuncbag, N.; Gursoy, A.; Nussinov, R.; Keskin, O. Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using PRISM. Nat. Protoc., 2011, 6(9), 1341-1354.
[http://dx.doi.org/10.1038/nprot.2011.367] [PMID: 21886100]
[63]
Kuzu, G.; Gursoy, A.; Nussinov, R.; Keskin, O. Exploiting conformational ensembles in modeling protein-protein interactions on the proteome scale. J. Proteome Res., 2013, 12(6), 2641-2653.
[http://dx.doi.org/10.1021/pr400006k] [PMID: 23590674]
[64]
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]
[65]
Alanis-Lobato, G.; Andrade-Navarro, M.A.; Schaefer, M.H. HIPPIE v2.0: Enhancing meaningfulness and reliability of protein-protein interaction networks. Nucleic Acids Res., 2017, 45(D1), D408-D414.
[http://dx.doi.org/10.1093/nar/gkw985] [PMID: 27794551]
[66]
Schaefer, M.H.; Fontaine, J.F.; Vinayagam, A.; Porras, P.; Wanker, E.E.; Andrade-Navarro, M.A. HIPPIE: Integrating protein interaction networks with experiment based quality scores. PLoS One, 2012, 7(2)e31826
[http://dx.doi.org/10.1371/journal.pone.0031826] [PMID: 22348130]
[67]
Vreven, T.; Hwang, H.; Pierce, B.G.; Weng, Z. Evaluating template-based and template-free protein-protein complex structure prediction. Brief. Bioinform., 2014, 15(2), 169-176.
[http://dx.doi.org/10.1093/bib/bbt047] [PMID: 23818491]
[68]
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]
[69]
Shoemaker, B.A.; Panchenko, A.R. Deciphering protein-protein interactions. Part I. Experimental techniques and databases. PLOS Comput. Biol., 2007, 3(3)e42
[http://dx.doi.org/10.1371/journal.pcbi.0030042] [PMID: 17397251]
[70]
Canduri, F.; de Azevedo, W.F. Protein crystallography in drug discovery. Curr. Drug Targets, 2008, 9(12), 1048-1053.
[http://dx.doi.org/10.2174/138945008786949423] [PMID: 19128214]
[71]
Fadel, V.; Bettendorff, P.; Herrmann, T.; de Azevedo, W.F., Jr; Oliveira, E.B.; Yamane, T.; Wüthrich, K. Automated NMR structure determination and disulfide bond identification of the myotoxin crotamine from Crotalus durissus terrificus. Toxicon, 2005, 46(7), 759-767.
[http://dx.doi.org/10.1016/j.toxicon.2005.07.018] [PMID: 16185738]
[72]
Yan, Y.; Marriott, G. Analysis of protein interactions using fluorescence technologies. Curr. Opin. Chem. Biol., 2003, 7(5), 635-640.
[http://dx.doi.org/10.1016/j.cbpa.2003.08.017] [PMID: 14580569]
[73]
Lacivita, E.; Leopoldo, M.; Berardi, F.; Colabufo, N.A.; Perrone, R. Activatable fluorescent probes: A new concept in optical molecular imaging. Curr. Med. Chem., 2012, 19(28), 4731-4741.
[http://dx.doi.org/10.2174/092986712803341511] [PMID: 22873661]
[74]
Filgueira de Azevedo, W., Jr; dos Santos, G.C.; dos Santos, D.M.; Olivieri, J.R.; Canduri, F.; Silva, R.G.; Basso, L.A.; Renard, G.; da Fonseca, I.O.; Mendes, M.A.; Palma, M.S.; Santos, D.S. Docking and small angle X-ray scattering studies of purine nucleoside phosphorylase. Biochem. Biophys. Res. Commun., 2003, 309(4), 923-928.
[http://dx.doi.org/10.1016/j.bbrc.2003.08.093] [PMID: 13679062]
[75]
Hura, G.L.; Menon, A.L.; Hammel, M.; Rambo, R.P.; Poole, F.L., II; Tsutakawa, S.E.; Jenney, F.E., Jr; Classen, S.; Frankel, K.A.; Hopkins, R.C.; Yang, S.J.; Scott, J.W.; Dillard, B.D.; Adams, M.W.; Tainer, J.A. Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS). Nat. Methods, 2009, 6(8), 606-612.
[http://dx.doi.org/10.1038/nmeth.1353] [PMID: 19620974]
[76]
Cooper, M.A. Label-free screening of bio-molecular interactions. Anal. Bioanal. Chem., 2003, 377(5), 834-842.
[http://dx.doi.org/10.1007/s00216-003-2111-y] [PMID: 12904946]
[77]
Podobnik, M.; Kraševec, N.; Bedina Zavec, A.; Naneh, O.; Flašker, A.; Caserman, S.; Hodnik, V.; Anderluh, G. How to study protein-protein interactions. Acta Chim. Slov., 2016, 63(3), 424-439.
[http://dx.doi.org/10.17344/acsi.2016.2419] [PMID: 27640371]
[78]
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]
[79]
Ito, T.; Chiba, T.; Ozawa, R.; Yoshida, M.; Hattori, M.; Sakaki, Y. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl. Acad. Sci. USA, 2001, 98(8), 4569-4574.
[http://dx.doi.org/10.1073/pnas.061034498] [PMID: 11283351]
[80]
Rigaut, G.; Shevchenko, A.; Rutz, B.; Wilm, M.; Mann, M.; Séraphin, B. A generic protein purification method for protein complex characterization and proteome exploration. Nat. Biotechnol., 1999, 17(10), 1030-1032.
[http://dx.doi.org/10.1038/13732] [PMID: 10504710]
[81]
Causier, B.; Davies, B. Analysing protein-protein interactions with the yeast two-hybrid system. Plant Mol. Biol., 2002, 50(6), 855-870.
[http://dx.doi.org/10.1023/A:1021214007897] [PMID: 12516858]
[82]
Rao, V.S.; Srinivas, K.; Sujini, G.N.; Kumar, G.N. Protein-protein interaction detection: Methods and analysis. Int. J. Proteomics, 2014.2014147648
[http://dx.doi.org/10.1155/2014/147648] [PMID: 24693427]
[83]
Csermely, P.; Korcsmáros, T.; Kiss, H.J.; London, G.; Nussinov, R. Structure and dynamics of molecular networks: A novel paradigm of drug discovery: A comprehensive review. Pharmacol. Ther., 2013, 138(3), 333-408.
[http://dx.doi.org/10.1016/j.pharmthera.2013.01.016] [PMID: 23384594]
[84]
Wodak, S.J.; Vlasblom, J.; Turinsky, A.L.; Pu, S. Protein-protein interaction networks: The puzzling riches. Curr. Opin. Struct. Biol., 2013, 23(6), 941-953.
[http://dx.doi.org/10.1016/j.sbi.2013.08.002] [PMID: 24007795]
[85]
von Mering, C.; Krause, R.; Snel, B.; Cornell, M.; Oliver, S.G.; Fields, S.; Bork, P. Comparative assessment of large-scale data sets of protein-protein interactions. Nature, 2002, 417(6887), 399-403.
[http://dx.doi.org/10.1038/nature750] [PMID: 12000970]
[86]
Turinsky, A.L.; Razick, S.; Turner, B.; Donaldson, I.M.; Wodak, S.J. Literature curation of protein interactions: Measuring agreement across major public databases. Database (Oxford), 2010, 2010, baq026.
[http://dx.doi.org/10.1093/database/baq026] [PMID: 21183497]
[87]
Huang, H.; Bader, J.S. Precision and recall estimates for two-hybrid screens. Bioinformatics, 2009, 25(3), 372-378.
[http://dx.doi.org/10.1093/bioinformatics/btn640] [PMID: 19091773]
[88]
Mrowka, R.; Patzak, A.; Herzel, H. Is there a bias in proteome research? Genome Res., 2001, 11(12), 1971-1973.
[http://dx.doi.org/10.1101/gr.206701] [PMID: 11731485]
[89]
Braun, P.; Tasan, M.; Dreze, M.; Barrios-Rodiles, M.; Lemmens, I.; Yu, H.; Sahalie, J.M.; Murray, R.R.; Roncari, L.; de Smet, A.S.; Venkatesan, K.; Rual, J.F.; Vandenhaute, J.; Cusick, M.E.; Pawson, T.; Hill, D.E.; Tavernier, J.; Wrana, J.L.; Roth, F.P.; Vidal, M. An experimentally derived confidence score for binary protein-protein interactions. Nat. Methods, 2009, 6(1), 91-97.
[http://dx.doi.org/10.1038/nmeth.1281] [PMID: 19060903]
[90]
Ivanic, J.; Yu, X.; Wallqvist, A.; Reifman, J. Influence of protein abundance on high-throughput protein-protein interaction detection. PLoS One, 2009, 4(6)e5815
[http://dx.doi.org/10.1371/journal.pone.0005815] [PMID: 19503833]
[91]
Mellacheruvu, D.; Wright, Z.; Couzens, A.L.; Lambert, J.P.; St-Denis, N.A.; Li, T.; Miteva, Y.V.; Hauri, S.; Sardiu, M.E.; Low, T.Y.; Halim, V.A.; Bagshaw, R.D.; Hubner, N.C.; Al-Hakim, A.; Bouchard, A.; Faubert, D.; Fermin, D.; Dunham, W.H.; Goudreault, M.; Lin, Z.Y.; Badillo, B.G.; Pawson, T.; Durocher, D.; Coulombe, B.; Aebersold, R.; Superti-Furga, G.; Colinge, J.; Heck, A.J.; Choi, H.; Gstaiger, M.; Mohammed, S.; Cristea, I.M.; Bennett, K.L.; Washburn, M.P.; Raught, B.; Ewing, R.M.; Gingras, A.C.; Nesvizhskii, A.I. The CRAPome: A contaminant repository for affinity purification-mass spectrometry data. Nat. Methods, 2013, 10(8), 730-736.
[http://dx.doi.org/10.1038/nmeth.2557] [PMID: 23921808]
[92]
Trabuco, L.G.; Betts, M.J.; Russell, R.B. Negative protein-protein interaction datasets derived from large-scale two-hybrid experiments. Methods, 2012, 58(4), 343-348.
[http://dx.doi.org/10.1016/j.ymeth.2012.07.028] [PMID: 22884951]
[93]
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]
[94]
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]
[95]
Ewing, R.M.; Chu, P.; Elisma, F.; Li, H.; Taylor, P.; Climie, S.; McBroom-Cerajewski, L.; Robinson, M.D.; O’Connor, L.; Li, M.; Taylor, R.; Dharsee, M.; Ho, Y.; Heilbut, A.; Moore, L.; Zhang, S.; Ornatsky, O.; Bukhman, Y.V.; Ethier, M.; Sheng, Y.; Vasilescu, J.; Abu-Farha, M.; Lambert, J.P.; Duewel, H.S.; Stewart, I.I.; Kuehl, B.; Hogue, K.; Colwill, K.; Gladwish, K.; Muskat, B.; Kinach, R.; Adams, S.L.; Moran, M.F.; Morin, G.B.; Topaloglou, T.; Figeys, D. Large-scale mapping of human protein-protein interactions by mass spectrometry. Mol. Syst. Biol., 2007, 3, 89.
[http://dx.doi.org/10.1038/msb4100134] [PMID: 17353931]
[96]
Li, S.; Armstrong, C.M.; Bertin, N.; Ge, H.; Milstein, S.; Boxem, M.; Vidalain, P.O.; Han, J.D.; Chesneau, A.; Hao, T.; Goldberg, D.S.; Li, N.; Martinez, M.; Rual, J.F.; Lamesch, P.; Xu, L.; Tewari, M.; Wong, S.L.; Zhang, L.V.; Berriz, G.F.; Jacotot, L.; Vaglio, P.; Reboul, J.; Hirozane-Kishikawa, T.; Li, Q.; Gabel, H.W.; Elewa, A.; Baumgartner, B.; Rose, D.J.; Yu, H.; Bosak, S.; Sequerra, R.; Fraser, A.; Mango, S.E.; Saxton, W.M.; Strome, S.; Van Den Heuvel, S.; Piano, F.; Vandenhaute, J.; Sardet, C.; Gerstein, M.; Doucette-Stamm, L.; Gunsalus, K.C.; Harper, J.W.; Cusick, M.E.; Roth, F.P.; Hill, D.E.; Vidal, M. A map of the interactome network of the metazoan C. elegans. Science, 2004, 303(5657), 540-543.
[http://dx.doi.org/10.1126/science.1091403] [PMID: 14704431]
[97]
Giot, L.; Bader, J.S.; Brouwer, C.; Chaudhuri, A.; Kuang, B.; Li, Y.; Hao, Y.L.; Ooi, C.E.; Godwin, B.; Vitols, E.; Vijayadamodar, G.; Pochart, P.; Machineni, H.; Welsh, M.; Kong, Y.; Zerhusen, B.; Malcolm, R.; Varrone, Z.; Collis, A.; Minto, M.; Burgess, S.; McDaniel, L.; Stimpson, E.; Spriggs, F.; Williams, J.; Neurath, K.; Ioime, N.; Agee, M.; Voss, E.; Furtak, K.; Renzulli, R.; Aanensen, N.; Carrolla, S.; Bickelhaupt, E.; Lazovatsky, Y.; DaSilva, A.; Zhong, J.; Stanyon, C.A.; Finley, R.L., Jr; White, K.P.; Braverman, M.; Jarvie, T.; Gold, S.; Leach, M.; Knight, J.; Shimkets, R.A.; McKenna, M.P.; Chant, J.; Rothberg, J.M. A protein interaction map of Drosophila melanogaster. Science, 2003, 302(5651), 1727-1736.
[http://dx.doi.org/10.1126/science.1090289] [PMID: 14605208]
[98]
Butland, G.; Peregrín-Alvarez, J.M.; Li, J.; Yang, W.; Yang, X.; Canadien, V.; Starostine, A.; Richards, D.; Beattie, B.; Krogan, N.; Davey, M.; Parkinson, J.; Greenblatt, J.; Emili, A. Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature, 2005, 433(7025), 531-537.
[http://dx.doi.org/10.1038/nature03239] [PMID: 15690043]
[99]
Arabidopsis Interactome Mapping Consortium. Evidence for network evolution in an Arabidopsis interactome map. Science, 2011, 333(6042), 601-607.
[http://dx.doi.org/10.1126/science.1203877] [PMID: 21798944]
[100]
Ideker, T.; Krogan, N.J. Differential network biology. Mol. Syst. Biol., 2012, 8, 565.
[http://dx.doi.org/10.1038/msb.2011.99] [PMID: 22252388]
[101]
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]
[102]
Nibbe, R.K.; Chowdhury, S.A.; Koyutürk, M.; Ewing, R.; Chance, M.R. Protein-protein interaction networks and subnetworks in the biology of disease. Wiley Interdiscip. Rev. Syst. Biol. Med., 2011, 3(3), 357-367.
[http://dx.doi.org/10.1002/wsbm.121] [PMID: 20865778]
[103]
Goehler, H.; Lalowski, M.; Stelzl, U.; Waelter, S.; Stroedicke, M.; Worm, U.; Droege, A.; Lindenberg, K.S.; Knoblich, M.; Haenig, C.; Herbst, M.; Suopanki, J.; Scherzinger, E.; Abraham, C.; Bauer, B.; Hasenbank, R.; Fritzsche, A.; Ludewig, A.H.; Büssow, K.; Coleman, S.H.; Gutekunst, C.A.; Landwehrmeyer, B.G.; Lehrach, H.; Wanker, E.E. A protein interaction network links GIT1, an enhancer of huntingtin aggregation, to Huntington’s disease. Mol. Cell, 2004, 15(6), 853-865.
[http://dx.doi.org/10.1016/j.molcel.2004.09.016] [PMID: 15383276]
[104]
Lim, J.; Hao, T.; Shaw, C.; Patel, A.J.; Szabó, G.; Rual, J.F.; Fisk, C.J.; Li, N.; Smolyar, A.; Hill, D.E.; Barabási, A.L.; Vidal, M.; Zoghbi, H.Y. A protein-protein interaction network for human inherited ataxias and disorders of Purkinje cell degeneration. Cell, 2006, 125(4), 801-814.
[http://dx.doi.org/10.1016/j.cell.2006.03.032] [PMID: 16713569]
[105]
Pujana, M.A.; Han, J.D.; Starita, L.M.; Stevens, K.N.; Tewari, M.; Ahn, J.S.; Rennert, G.; Moreno, V.; Kirchhoff, T.; Gold, B.; Assmann, V.; Elshamy, W.M.; Rual, J.F.; Levine, D.; Rozek, L.S.; Gelman, R.S.; Gunsalus, K.C.; Greenberg, R.A.; Sobhian, B.; Bertin, N.; Venkatesan, K.; Ayivi-Guedehoussou, N.; Solé, X.; Hernández, P.; Lázaro, C.; Nathanson, K.L.; Weber, B.L.; Cusick, M.E.; Hill, D.E.; Offit, K.; Livingston, D.M.; Gruber, S.B.; Parvin, J.D.; Vidal, M. Network modeling links breast cancer susceptibility and centrosome dysfunction. Nat. Genet., 2007, 39(11), 1338-1349.
[http://dx.doi.org/10.1038/ng.2007.2] [PMID: 17922014]
[106]
Nibbe, R.K.; Markowitz, S.; Myeroff, L.; Ewing, R.; Chance, M.R. Discovery and scoring of protein interaction subnetworks discriminative of late stage human colon cancer. Mol. Cell. Proteomics, 2009, 8(4), 827-845.
[http://dx.doi.org/10.1074/mcp.M800428-MCP200] [PMID: 19098285]
[107]
Brehme, M.; Voisine, C.; Rolland, T.; Wachi, S.; Soper, J.H.; Zhu, Y.; Orton, K.; Villella, A.; Garza, D.; Vidal, M.; Ge, H.; Morimoto, R.I. A chaperome subnetwork safeguards proteostasis in aging and neurodegenerative disease. Cell Rep., 2014, 9(3), 1135-1150.
[http://dx.doi.org/10.1016/j.celrep.2014.09.042] [PMID: 25437566]
[108]
Kerrien, S.; Aranda, B.; Breuza, L.; Bridge, A.; Broackes-Carter, F.; Chen, C.; Duesbury, M.; Dumousseau, M.; Feuermann, M.; Hinz, U.; Jandrasits, C.; Jimenez, R.C.; Khadake, J.; Mahadevan, U.; Masson, P.; Pedruzzi, I.; Pfeiffenberger, E.; Porras, P.; Raghunath, A.; Roechert, B.; Orchard, S.; Hermjakob, H. The IntAct molecular interaction database in 2012. Nucleic Acids Res., 2012, 40(Database issue), D841-D846.
[http://dx.doi.org/10.1093/nar/gkr1088] [PMID: 22121220]
[109]
Cusick, M.E.; Yu, H.; Smolyar, A.; Venkatesan, K.; Carvunis, A.R.; Simonis, N.; Rual, J.F.; Borick, H.; Braun, P.; Dreze, M.; Vandenhaute, J.; Galli, M.; Yazaki, J.; Hill, D.E.; Ecker, J.R.; Roth, F.P.; Vidal, M. Literature-curated protein interaction datasets. Nat. Methods, 2009, 6(1), 39-46.
[http://dx.doi.org/10.1038/nmeth.1284] [PMID: 19116613]
[110]
Orchard, S.; Kerrien, S.; Abbani, S.; Aranda, B.; Bhate, J.; Bidwell, S.; Bridge, A.; Briganti, L.; Brinkman, F.S.; Cesareni, G.; Chatr-aryamontri, A.; Chautard, E.; Chen, C.; Dumousseau, M.; Goll, J.; Hancock, R.E.; Hannick, L.I.; Jurisica, I.; Khadake, J.; Lynn, D.J.; Mahadevan, U.; Perfetto, L.; Raghunath, A.; Ricard-Blum, S.; Roechert, B.; Salwinski, L.; Stümpflen, V.; Tyers, M.; Uetz, P.; Xenarios, I.; Hermjakob, H. Protein interaction data curation: The International Molecular Exchange (IMEx) consortium. Nat. Methods, 2012, 9(4), 345-350.
[http://dx.doi.org/10.1038/nmeth.1931] [PMID: 22453911]
[111]
Aranda, B.; Blankenburg, H.; Kerrien, S.; Brinkman, F.S.; Ceol, A.; Chautard, E.; Dana, J.M.; De Las Rivas, J.; Dumousseau, M.; Galeota, E.; Gaulton, A.; Goll, J.; Hancock, R.E.; Isserlin, R.; Jimenez, R.C.; Kerssemakers, J.; Khadake, J.; Lynn, D.J.; Michaut, M.; O’Kelly, G.; Ono, K.; Orchard, S.; Prieto, C.; Razick, S.; Rigina, O.; Salwinski, L.; Simonovic, M.; Velankar, S.; Winter, A.; Wu, G.; Bader, G.D.; Cesareni, G.; Donaldson, I.M.; Eisenberg, D.; Kleywegt, G.J.; Overington, J.; Ricard-Blum, S.; Tyers, M.; Albrecht, M.; Hermjakob, H. PSICQUIC and PSISCORE: Accessing and scoring molecular interactions. Nat. Methods, 2011, 8(7), 528-529.
[http://dx.doi.org/10.1038/nmeth.1637] [PMID: 21716279]
[112]
Sowmya, G.; Ranganathan, S. Protein-protein interactions and prediction: A comprehensive overview. Protein Pept. Lett., 2014, 21(8), 779-789.
[http://dx.doi.org/10.2174/09298665113209990056] [PMID: 23855658]
[113]
Keshava Prasad, T.S.; Goel, R.; Kandasamy, K.; Keerthikumar, S.; Kumar, S.; Mathivanan, S.; Telikicherla, D.; Raju, R.; Shafreen, B.; Venugopal, A.; Balakrishnan, L.; Marimuthu, A.; Banerjee, S.; Somanathan, D.S.; Sebastian, A.; Rani, S.; Ray, S.; Harrys Kishore, C.J.; Kanth, S.; Ahmed, M.; Kashyap, M.K.; Mohmood, R.; Ramachandra, Y.L.; Krishna, V.; Rahiman, B.A.; Mohan, S.; Ranganathan, P.; Ramabadran, S.; Chaerkady, R.; Pandey, A. Human Protein Reference Database--2009 update. Nucleic Acids Res., 2009, 37(Database issue), D767-D772.
[http://dx.doi.org/10.1093/nar/gkn892] [PMID: 18988627]
[114]
Güldener, U.; Münsterkötter, M.; Oesterheld, M.; Pagel, P.; Ruepp, A.; Mewes, H.W.; Stümpflen, V. MPact: The MIPS protein interaction resource on yeast. Nucleic Acids Res., 2006, 34(Database issue), D436-D441.
[http://dx.doi.org/10.1093/nar/gkj003] [PMID: 16381906]
[115]
Pagel, P.; Kovac, S.; Oesterheld, M.; Brauner, B.; Dunger-Kaltenbach, I.; Frishman, G.; Montrone, C.; Mark, P.; Stümpflen, V.; Mewes, H.W.; Ruepp, A.; Frishman, D. The MIPS mammalian protein-protein interaction database. Bioinformatics, 2005, 21(6), 832-834.
[http://dx.doi.org/10.1093/bioinformatics/bti115] [PMID: 15531608]
[116]
Goll, J.; Rajagopala, S.V.; Shiau, S.C.; Wu, H.; Lamb, B.T.; Uetz, P. MPIDB: The microbial protein interaction database. Bioinformatics, 2008, 24(15), 1743-1744.
[http://dx.doi.org/10.1093/bioinformatics/btn285] [PMID: 18556668]
[117]
Licata, L.; Briganti, L.; Peluso, D.; Perfetto, L.; Iannuccelli, M.; Galeota, E.; Sacco, F.; Palma, A.; Nardozza, A.P.; Santonico, E.; Castagnoli, L.; Cesareni, G. MINT, the molecular interaction database: 2012 update. Nucleic Acids Res., 2012, 40(Database issue), D857-D861.
[http://dx.doi.org/10.1093/nar/gkr930] [PMID: 22096227]
[118]
Bader, G.D.; Donaldson, I.; Wolting, C.; Ouellette, B.F.; Pawson, T.; Hogue, C.W. BIND--The Biomolecular Interaction Network Database. Nucleic Acids Res., 2001, 29(1), 242-245.
[http://dx.doi.org/10.1093/nar/29.1.242] [PMID: 11125103]
[119]
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]
[120]
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]
[121]
Hermjakob, H.; Montecchi-Palazzi, L.; Lewington, C.; Mudali, S.; Kerrien, S.; Orchard, S.; Vingron, M.; Roechert, B.; Roepstorff, P.; Valencia, A.; Margalit, H.; Armstrong, J.; Bairoch, A.; Cesareni, G.; Sherman, D.; Apweiler, R. IntAct: An open source molecular interaction database. Nucleic Acids Res., 2004, 32(Database issue), D452-D455.
[http://dx.doi.org/10.1093/nar/gkh052] [PMID: 14681455]
[122]
Kerrien, S.; Alam-Faruque, Y.; Aranda, B.; Bancarz, I.; Bridge, A.; Derow, C.; Dimmer, E.; Feuermann, M.; Friedrichsen, A.; Huntley, R.; Kohler, C.; Khadake, J.; Leroy, C.; Liban, A.; Lieftink, C.; Montecchi-Palazzi, L.; Orchard, S.; Risse, J.; Robbe, K.; Roechert, B.; Thorneycroft, D.; Zhang, Y.; Apweiler, R.; Hermjakob, H. IntAct--open source resource for molecular interaction data. Nucleic Acids Res., 2007, 35(Database issue), D561-D565.
[http://dx.doi.org/10.1093/nar/gkl958] [PMID: 17145710]
[123]
Chatr-Aryamontri, A.; Oughtred, R.; Boucher, L.; Rust, J.; Chang, C.; Kolas, N.K.; O’Donnell, L.; Oster, S.; Theesfeld, C.; Sellam, A.; Stark, C.; Breitkreutz, B.J.; Dolinski, K.; Tyers, M. The BioGRID interaction database: 2017 update. Nucleic Acids Res., 2017, 45(D1), D369-D379.
[http://dx.doi.org/10.1093/nar/gkw1102] [PMID: 27980099]
[124]
Islamaj Doğan, R.; Kim, S.; Chatr-Aryamontri, A.; Chang, C.S.; Oughtred, R.; Rust, J.; Wilbur, W.J.; Comeau, D.C.; Dolinski, K.; Tyers, M. The BioC-BioGRID corpus: Full text articles annotated for curation of protein-protein and genetic interactions. Database (Oxford),, 2017, 017, baw147.
[http://dx.doi.org/10.1093/database/baw147] [PMID: 28077563]
[125]
Alonso-López, D.; Gutiérrez, M.A.; Lopes, K.P.; Prieto, C.; Santamaría, R.; De Las Rivas, J. APID interactomes: Providing proteome-based interactomes with controlled quality for multiple species and derived networks. Nucleic Acids Res., 2016, 44(W1)W529-35
[http://dx.doi.org/10.1093/nar/gkw363] [PMID: 27131791]
[126]
Calderone, A.; Castagnoli, L.; Cesareni, G. mentha: A resource for browsing integrated protein-interaction networks. Nat. Methods, 2013, 10(8), 690-691.
[http://dx.doi.org/10.1038/nmeth.2561] [PMID: 23900247]
[127]
Razick, S.; Magklaras, G.; Donaldson, I.M. iRefIndex: A consolidated protein interaction database with provenance. BMC Bioinformatics, 2008, 9, 405.
[http://dx.doi.org/10.1186/1471-2105-9-405] [PMID: 18823568]
[128]
Turner, B.; Razick, S.; Turinsky, A.L.; Vlasblom, J.; Crowdy, E.K.; Cho, E.; Morrison, K.; Donaldson, I.M.; Wodak, S.J. iRefWeb: Interactive analysis of consolidated protein interaction data and their supporting evidence. Database (Oxford),, 2010, 2010, baq023.
[http://dx.doi.org/10.1093/database/baq023] [PMID: 20940177]
[129]
Kalathur, R.K.; Pinto, J.P.; Hernández-Prieto, M.A.; Machado, R.S.; Almeida, D.; Chaurasia, G.; Futschik, M.E. UniHI 7: An enhanced database for retrieval and interactive analysis of human molecular interaction networks. Nucleic Acids Res., 2014, 42(Database issue), D408-D414.
[http://dx.doi.org/10.1093/nar/gkt1100] [PMID: 24214987]
[130]
Calderone, A.; Licata, L.; Cesareni, G. VirusMentha: A new resource for virus-host protein interactions. Nucleic Acids Res., 2015, 43(Database issue), D588-D592.
[http://dx.doi.org/10.1093/nar/gku830] [PMID: 25217587]
[131]
Guirimand, T.; Delmotte, S.; Navratil, V. VirHostNet 2.0: Surfing on the web of virus/host molecular interactions data. Nucleic Acids Res., 2015, 43(Database issue), D583-D587.
[http://dx.doi.org/10.1093/nar/gku1121] [PMID: 25392406]
[132]
Kumar, R.; Nanduri, B. HPIDB--a unified resource for host-pathogen interactions. BMC Bioinformatics, 2010, 11(Suppl. 6), S16.
[http://dx.doi.org/10.1186/1471-2105-11-S6-S16] [PMID: 20946599]
[133]
Geisler-Lee, J.; O’Toole, N.; Ammar, R.; Provart, N.J.; Millar, A.H.; Geisler, M. A predicted interactome for Arabidopsis. Plant Physiol., 2007, 145(2), 317-329.
[http://dx.doi.org/10.1104/pp.107.103465] [PMID: 17675552]
[134]
Launay, G.; Salza, R.; Multedo, D.; Thierry-Mieg, N.; Ricard-Blum, S. MatrixDB, the extracellular matrix interaction database: Updated content, a new navigator and expanded functionalities. Nucleic Acids Res., 2015, 43(Database issue), D321-D327.
[http://dx.doi.org/10.1093/nar/gku1091] [PMID: 25378329]
[135]
Breuer, K.; Foroushani, A.K.; Laird, M.R.; Chen, C.; Sribnaia, A.; Lo, R.; Winsor, G.L.; Hancock, R.E.; Brinkman, F.S.; Lynn, D.J.; Innate, D.B. Systems biology of innate immunity and beyond--recent updates and continuing curation. Nucleic Acids Res., 2013, 41(Database issue), D1228-D1233.
[http://dx.doi.org/10.1093/nar/gks1147] [PMID: 23180781]
[136]
Meldal, B.H.; Forner-Martinez, O.; Costanzo, M.C.; Dana, J.; Demeter, J.; Dumousseau, M.; Dwight, S.S.; Gaulton, A.; Licata, L.; Melidoni, A.N.; Ricard-Blum, S.; Roechert, B.; Skyzypek, M.S.; Tiwari, M.; Velankar, S.; Wong, E.D.; Hermjakob, H.; Orchard, S. The complex portal--an encyclopaedia of macromolecular complexes. Nucleic Acids Res., 2015, 43(Database issue), D479-D484.
[http://dx.doi.org/10.1093/nar/gku975] [PMID: 25313161]
[137]
Ruepp, A.; Waegele, B.; Lechner, M.; Brauner, B.; Dunger-Kaltenbach, I.; Fobo, G.; Frishman, G.; Montrone, C.; Mewes, H.W. CORUM: The comprehensive resource of mammalian protein complexes--2009. Nucleic Acids Res., 2010, 38(Database issue), D497-D501.
[http://dx.doi.org/10.1093/nar/gkp914] [PMID: 19884131]
[138]
Berman, H.M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T.N.; Weissig, H.; Shindyalov, I.N.; Bourne, P.E. The Protein Data Bank. Nucleic Acids Res., 2000, 28(1), 235-242.
[http://dx.doi.org/10.1093/nar/28.1.235] [PMID: 10592235]
[139]
Winter, C.; Henschel, A.; Tuukkanen, A.; Schroeder, M. Protein interactions in 3D: From interface evolution to drug discovery. J. Struct. Biol., 2012, 179(3), 347-358.
[http://dx.doi.org/10.1016/j.jsb.2012.04.009] [PMID: 22595401]
[140]
Winter, C.; Henschel, A.; Kim, W.K.; Schroeder, M. SCOPPI: A structural classification of protein-protein interfaces. Nucleic Acids Res., 2006, 34(Database issue), D310-D314.
[http://dx.doi.org/10.1093/nar/gkj099] [PMID: 16381874]
[141]
Finn, R.D.; Miller, B.L.; Clements, J.; Bateman, A. iPfam: A database of protein family and domain interactions found in the Protein Data Bank. Nucleic Acids Res., 2014, 42(Database issue), D364-D373.
[http://dx.doi.org/10.1093/nar/gkt1210] [PMID: 24297255]
[142]
Davis, F.P.; Sali, A. PIBASE: A comprehensive database of structurally defined protein interfaces. Bioinformatics, 2005, 21(9), 1901-1907.
[http://dx.doi.org/10.1093/bioinformatics/bti277] [PMID: 15657096]
[143]
Mosca, R.; Céol, A.; Stein, A.; Olivella, R.; Aloy, P. 3did: A catalog of domain-based interactions of known three-dimensional structure. Nucleic Acids Res., 2014, 42(Database issue), D374-D379.
[http://dx.doi.org/10.1093/nar/gkt887] [PMID: 24081580]
[144]
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.
[http://dx.doi.org/10.1093/database/bat039] [PMID: 23766369]
[145]
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.
[http://dx.doi.org/10.1093/database/baw007] [PMID: 26980515]
[146]
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]
[147]
Meyer, M.J.; Das, J.; Wang, X.; Yu, H. INstruct: A database of high-quality 3D structurally resolved protein interactome networks. Bioinformatics, 2013, 29(12), 1577-1579.
[http://dx.doi.org/10.1093/bioinformatics/btt181] [PMID: 23599502]
[148]
Mosca, R.; Céol, A.; Aloy, P. Interactome3D: Adding structural details to protein networks. Nat. Methods, 2013, 10(1), 47-53.
[http://dx.doi.org/10.1038/nmeth.2289] [PMID: 23399932]
[149]
Szklarczyk, D.; Franceschini, A.; Kuhn, M.; Simonovic, M.; Roth, A.; Minguez, P.; Doerks, T.; Stark, M.; Muller, J.; Bork, P.; Jensen, L.J.; von Mering, C. The STRING database in 2011: Functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res., 2011, 39(Database issue), D561-D568.
[http://dx.doi.org/10.1093/nar/gkq973] [PMID: 21045058]
[150]
Szklarczyk, D.; Franceschini, A.; Wyder, S.; Forslund, K.; Heller, D.; Huerta-Cepas, J.; Simonovic, M.; Roth, A.; Santos, A.; Tsafou, K.P.; Kuhn, M.; Bork, P.; Jensen, L.J.; von Mering, C. STRING v10: Protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Res., 2015, 43(Database issue), D447-D452.
[http://dx.doi.org/10.1093/nar/gku1003] [PMID: 25352553]
[151]
Planas-Iglesias, J.; Guney, E.; García-García, J.; Robertson, K.A.; Raza, S.; Freeman, T.C.; Ghazal, P.; Oliva, B. Extending signaling pathways with protein-interaction networks. Application to apoptosis. OMICS, 2012, 16(5), 245-256.
[http://dx.doi.org/10.1089/omi.2011.0130] [PMID: 22385281]
[152]
Brown, K.R.; Jurisica, I. Unequal evolutionary conservation of human protein interactions in interologous networks. Genome Biol., 2007, 8(5), R95.
[http://dx.doi.org/10.1186/gb-2007-8-5-r95] [PMID: 17535438]
[153]
Kotlyar, M.; Pastrello, C.; Sheahan, N.; Jurisica, I. Integrated interactions database: Tissue-specific view of the human and model organism interactomes. Nucleic Acids Res., 2016, 44(D1), D536-D541.
[http://dx.doi.org/10.1093/nar/gkv1115] [PMID: 26516188]
[154]
Warde-Farley, D.; Donaldson, S.L.; Comes, O.; Zuberi, K.; Badrawi, R.; Chao, P.; Franz, M.; Grouios, C.; Kazi, F.; Lopes, C.T.; Maitland, A.; Mostafavi, S.; Montojo, J.; Shao, Q.; Wright, G.; Bader, G.D.; Morris, Q. The GeneMANIA prediction server: Biological network integration for gene prioritization and predicting gene function. Nucleic Acids Res,, 2010, 38(Web Server issue), W214-W220. .
[http://dx.doi.org/10.1093/nar/gkq537]
[155]
Kamburov, A.; Stelzl, U.; Lehrach, H.; Herwig, R. The ConsensusPathDB interaction database: 2013 update. Nucleic Acids Res., 2013, 41(Database issue), D793-D800.
[http://dx.doi.org/10.1093/nar/gks1055] [PMID: 23143270]
[156]
Smoot, M.E.; Ono, K.; Ruscheinski, J.; Wang, P.L.; Ideker, T. Cytoscape 2.8: New features for data integration and network visualization. Bioinformatics, 2011, 27(3), 431-432.
[http://dx.doi.org/10.1093/bioinformatics/btq675] [PMID: 21149340]
[157]
Garcia-Garcia, J.; Guney, E.; Aragues, R.; Planas-Iglesias, J.; Oliva, B. Biana: A software framework for compiling biological interactions and analyzing networks. BMC Bioinformatics, 2010, 11, 56.
[http://dx.doi.org/10.1186/1471-2105-11-56] [PMID: 20105306]
[158]
Nishida, K.; Ono, K.; Kanaya, S.; Takahashi, K. KEGGscape: A Cytoscape app for pathway data integration. F1000 Res., 2014, 3, 144.
[http://dx.doi.org/10.12688/f1000research.4524.1] [PMID: 25177485]
[159]
Maere, S.; Heymans, K.; Kuiper, M. BiNGO: A Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics, 2005, 21(16), 3448-3449.
[http://dx.doi.org/10.1093/bioinformatics/bti551] [PMID: 15972284]

Rights & Permissions Print Cite
Article Metrics
72
9
1
1
© 2024 Bentham Science Publishers | Privacy Policy