Building macromolecular assemblies by information-driven docking: Introducing the haddock multibody docking server

Molecular and Cellular Proteomics

Volumn 9, Issue 8, 2010, Pages 1784-1794

  Karaca, Ezgi ^a   Melquiond, Adrien S J ^a   De Vries, Sjoerd J ^a   Kastritis, Panagiotis L ^a   Bonvin, Alexandre M J J ^a  

^a UTRECHT UNIVERSITY   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

HOMODIMER DOUBLE STRANDED DNA; HOMOPENTAMER; HOMOTETRAMER; HOMOTRIMER; OLIGOMER; UNCLASSIFIED DRUG; AMINO ACID; MACROMOLECULE; MULTIPROTEIN COMPLEX;

ARTICLE; CHEMICAL MUTAGENESIS; CRYOELECTRON MICROSCOPY; DEUTERIUM HYDROGEN EXCHANGE; DNA PROTEIN COMPLEX; HIGH AMBIGUITY DRIVEN DOCKING; HUMAN; MACROMOLECULE; MASS SPECTROMETRY; MOLECULAR DOCKING; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTEIN ASSEMBLY; PROTEIN DNA INTERACTION; PROTEIN FUNCTION; SCORING SYSTEM; STRUCTURAL BIOINFORMATICS; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER INTERFACE; INTERNET; METABOLISM; PROCEDURES; X RAY CRYSTALLOGRAPHY;

AMINO ACIDS; COMPUTATIONAL BIOLOGY; CRYSTALLOGRAPHY, X-RAY; INTERNET; MACROMOLECULAR SUBSTANCES; MODELS, MOLECULAR; MULTIPROTEIN COMPLEXES; USER-COMPUTER INTERFACE;

EID: 77955371384     PISSN: 15359476     EISSN: 15359484     Source Type: Journal    
DOI: 10.1074/mcp.M000051-MCP201     Document Type: Article

References (71)

1. Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M. C., Baldwin, J., Devon, K., Dewar, K., Doyle, M., FitzHugh, W., Funke, R., Gage, D., Harris, K., Heaford, A., Howland, J., Kann, L., Lehoczky, J., LeVine, R., McEwan, P., McKernan, K., Meldrim, J., Mesirov, J. P., Miranda, C., Morris, W., Naylor, J., Raymond, C., Rosetti, M., Santos, R., Sheridan, A., Sougnez, C., Stange-Thomann, N., Stojanovic, N., Subramanian, A., Wyman, D., Rogers, J., Sulston, J., Ainscough, R., Beck, S., Bentley, D., Burton, J., Clee, C., Carter, N., Coulson, A., Deadman, R., Deloukas, P., Dunham, A., Dunham, I., Durbin, R., French, L., Grafham, D., Gregory, S., Hubbard, T., Humphray, S., Hunt, A., Jones, M., Lloyd, C., McMurray, A., Matthews, L., Mercer, S., Milne, S., Mullikin, J. C., Mungall, A., Plumb, R., Ross, M., Shownkeen, R., Sims, S., Waterston, R. H., Wilson, R. K., Hillier, L. W., McPherson, J. D., Marra, M. A., Mardis, E. R., Fulton, L. A., Chinwalla, A. T., Pepin, K. H., Gish, W. R., Chissoe, S. L., Wendl, M. C., Delehaunty, K. D., Miner, T. L., Delehaunty, A., Kramer, J. B., Cook, L. L., Fulton, R. S., Johnson, D. L., Minx, P. J., Clifton, S. W., Hawkins, T., Branscomb, E., Predki, P., Richardson, P., Wenning, S., Slezak, T., Doggett, N., Cheng, J. F., Olsen, A., Lucas, S., Elkin, C., Uberbacher, E., Frazier, M., Gibbs, R. A., Muzny, D. M., Scherer, S. E., Bouck, J. B., Sodergren, E. J., Worley, K. C., Rives, C. M., Gorrell, J. H., Metzker, M. L., Naylor, S. L., Kucherlapati, R. S., Nelson, D. L., Weinstock, G. M., Sakaki, Y., Fujiyama, A., Hattori, M., Yada, T., Toyoda, A., Itoh, T., Kawagoe, C., Watanabe, H., Totoki, Y., Taylor, T., Weissenbach, J., Heilig, R., Saurin, W., Artiguenave, F., Brottier, P., Bruls, T., Pelletier, E., Robert, C., Wincker, P., Smith, D. R., Doucette-Stamm, L., Rubenfield, M., Weinstock, K., Lee, H. M., Dubois, J., Rosenthal, A., Platzer, M., Nyakatura, G., Taudien, S., Rump, A., Yang, H., Yu, J., Wang, J., Huang, G., Gu, J., Hood, L., Rowen, L., Madan, A., Qin, S., Davis, R. W., Federspiel, N. A., Abola, A. P., Proctor, M. J., Myers, R. M., Schmutz, J., Dickson, M., Grimwood, J., Cox, D. R., Olson, M. V., Kaul, R., Raymond, C., Shimizu, N., Kawasaki, K., Minoshima, S., Evans, G. A., Athanasiou, M., Schultz, R., Roe, B. A., Chen, F., Pan, H., Ramser, J., Lehrach, H., Reinhardt, R., McCombie, W. R., de la Bastide, M., Dedhia, N., Blöcker, H., Hornischer, K., Nordsiek, G., Agarwala, R., Aravind, L., Bailey, J. A., Bateman, A., Batzoglou, S., Birney, E., Bork, P., Brown, D. G., Burge, C. B., Cerutti, L., Chen, H. C., Church, D., Clamp, M., Copley, R. R., Doerks, T., Eddy, S. R., Eichler, E. E., Furey, T. S., Galagan, J., Gilbert, J. G., Harmon, C., Hayashizaki, Y., Haussler, D., Hermjakob, H., Hokamp, K., Jang, W., Johnson, L. S., Jones, T. A., Kasif, S., Kaspryzk, A., Kennedy, S., Kent, W. J., Kitts, P., Koonin, E. V., Korf, I., Kulp, D., Lancet, D., Lowe, T. M., McLysaght, A., Mikkelsen, T., Moran, J. V., Mulder, N., Pollara, V. J., Ponting, C. P., Schuler, G., Schultz, J., Slater, G., Smit, A. F., Stupka, E., Szustakowski, J., Thierry-Mieg, D., Thierry- Mieg, J., Wagner, L., Wallis, J., Wheeler, R., Williams, A., Wolf, Y. I., Wolfe, K. H., Yang, S. P., Yeh, R. F., Collins, F., Guyer, M. S., Peterson, J., Felsenfeld, A., Wetterstrand, K. A., Patrinos, A., Morgan, M. J., de Jong, P., Catanese, J. J., Osoegawa, K., Shizuya, H., Choi, S., Chen, Y. J., and Szustakowki, J. (2001) Initial sequencing and analysis of the human genome. Nature 409, 860-921 (Pubitemid 32165345)
2. Venter, J. C., Adams, M. D., Myers, E. W., Li, P. W., Mural, R. J., Sutton, G. G., Smith, H. O., Yandell, M., Evans, C. A., Holt, R. A., Gocayne, J. D., Amanatides, P., Ballew, R. M., Huson, D. H., Wortman, J. R., Zhang, Q., Kodira, C. D., Zheng, X. H., Chen, L., Skupski, M., Subramanian, G., Thomas, P. D., Zhang, J., Gabor Miklos, G. L., Nelson, C., Broder, S., Clark, A. G., Nadeau, J., McKusick, V. A., Zinder, N., Levine, A. J., Roberts, R. J., Simon, M., Slayman, C., Hunkapiller, M., Bolanos, R., Delcher, A., Dew, I., Fasulo, D., Flanigan, M., Florea, L., Halpern, A., Hannenhalli, S., Kravitz, S., Levy, S., Mobarry, C., Reinert, K., Remington, K., Abu-Threideh, J., Beasley, E., Biddick, K., Bonazzi, V., Brandon, R., Cargill, M., Chandramouliswaran, I., Charlab, R., Chaturvedi, K., Deng, Z., Di Francesco, V., Dunn, P., Eilbeck, K., Evangelista, C., Gabrielian, A. E., Gan, W., Ge, W., Gong, F., Gu, Z., Guan, P., Heiman, T. J., Higgins, M. E., Ji, R. R., Ke, Z., Ketchum, K. A., Lai, Z., Lei, Y., Li, Z., Li, J., Liang, Y., Lin, X., Lu, F., Merkulov, G. V., Milshina, N., Moore, H. M., Naik, A. K., Narayan, V. A., Neelam, B., Nusskern, D., Rusch, D. B., Salzberg, S., Shao, W., Shue, B., Sun, J., Wang, Z., Wang, A., Wang, X., Wang, J., Wei, M., Wides, R., Xiao, C., Yan, C., Yao, A., Ye, J., Zhan, M., Zhang, W., Zhang, H., Zhao, Q., Zheng, L., Zhong, F., Zhong, W., Zhu, S., Zhao, S., Gilbert, D., Baumhueter, S., Spier, G., Carter, C., Cravchik, A., Woodage, T., Ali, F., An, H., Awe, A., Baldwin, D., Baden, H., Barnstead, M., Barrow, I., Beeson, K., Busam, D., Carver, A., Center, A., Cheng, M. L., Curry, L., Danaher, S., Davenport, L., Desilets, R., Dietz, S., Dodson, K., Doup, L., Ferriera, S., Garg, N., Gluecksmann, A., Hart, B., Haynes, J., Haynes, C., Heiner, C., Hladun, S., Hostin, D., Houck, J., Howland, T., Ibegwam, C., Johnson, J., Kalush, F., Kline, L., Koduru, S., Love, A., Mann, F., May, D., McCawley, S., McIntosh, T., McMullen, I., Moy, M., Moy, L., Murphy, B., Nelson, K., Pfannkoch, C., Pratts, E., Puri, V., Qureshi, H., Reardon, M., Rodriguez, R., Rogers, Y. H., Romblad, D., Ruhfel, B., Scott, R., Sitter, C., Smallwood, M., Stewart, E., Strong, R., Suh, E., Thomas, R., Tint, N. N., Tse, S., Vech, C., Wang, G., Wetter, J., Williams, S., Williams, M., Windsor, S., Winn-Deen, E., Wolfe, K., Zaveri, J., Zaveri, K., Abril, J. F., Guigó, R., Campbell, M. J., Sjolander, K. V., Karlak, B., Kejariwal, A., Mi, H., Lazareva, B., Hatton, T., Narechania, A., Diemer, K., Muruganujan, A., Guo, N., Sato, S., Bafna, V., Istrail, S., Lippert, R., Schwartz, R., Walenz, B., Yooseph, S., Allen, D., Basu, A., Baxendale, J., Blick, L., Caminha, M., Carnes-Stine, J., Caulk, P., Chiang, Y. H., Coyne, M., Dahlke, C., Mays, A., Dombroski, M., Donnelly, M., Ely, D., Esparham, S., Fosler, C., Gire, H., Glanowski, S., Glasser, K., Glodek, A., Gorokhov, M., Graham, K., Gropman, B., Harris, M., Heil, J., Henderson, S., Hoover, J., Jennings, D., Jordan, C., Jordan, J., Kasha, J., Kagan, L., Kraft, C., Levitsky, A., Lewis, M., Liu, X., Lopez, J., Ma, D., Majoros, W., McDaniel, J., Murphy, S., Newman, M., Nguyen, T., Nguyen, N., Nodell, M., Pan, S., Peck, J., Peterson, M., Rowe, W., Sanders, R., Scott, J., Simpson, M., Smith, T., Sprague, A., Stockwell, T., Turner, R., Venter, E., Wang, M., Wen, M., Wu, D., Wu, M., Xia, A., Zandieh, A., and Zhu, X. (2001) The sequence of the human genome. Science 291, 1304-1351
3. Xie, L., and Bourne, P. E. (2005) Functional coverage of the human genome by existing structures, structural genomics targets, and homology models. PLoS Comput. Biol. 1, e31
4. Alber, F., Förster, F., Korkin, D., Topf, M., and Sali, A. (2008) Integrating diverse data for structure determination of macromolecular assemblies. Annu. Rev. Biochem. 77, 443-477
5. Mueller, M., Jenni, S., and Ban, N. (2007) Strategies for crystallization and structure determination of very large macromolecular assemblies. Curr. Opin. Struct. Biol. 17, 572-579
6. Collins, S. R., Kemmeren, P., Zhao, X. C., Greenblatt, J. F., Spencer, F., Holstege, F. C., Weissman, J. S., and Krogan, N. J. (2007) Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae. Mol. Cell. Proteomics 6, 439-450
7. Krogan, N. J., Cagney, G., Yu, H., Zhong, G., Guo, X., Ignatchenko, A., Li, J., Pu, S., Datta, N., Tikuisis, A. P., Punna, T., Peregrín-Alvarez, J. M., Shales, M., Zhang, X., Davey, M., Robinson, M. D., Paccanaro, A., Bray, J. E., Sheung, A., Beattie, B., Richards, D. P., Canadien, V., Lalev, A., Mena, F., Wong, P., Starostine, A., Canete, M. M., Vlasblom, J., Wu, S., Orsi, C., Collins, S. R., Chandran, S., Haw, R., Rilstone, J. J., Gandi, K., Thompson, N. J., Musso, G., St Onge, P., Ghanny, S., Lam, M. H., Butland, G., Altaf-Ul, A. M., Kanaya, S., Shilatifard, A., O'Shea, E., Weissman, J. S., Ingles, C. J., Hughes, T. R., Parkinson, J., Gerstein, M., Wodak, S. J., Emili, A., and Greenblatt, J. F. (2006) Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440, 637-643
8. van Dijk, A. D., Kaptein, R., Boelens, R., and Bonvin, A. M. (2006) Combining NMR relaxation with chemical shift perturbation data to drive proteinprotein docking. J. Biomol. NMR 34, 237-244
9. van Dijk, A. D., Fushman, D., and Bonvin, A. M. (2005) Various strategies of using residual dipolar couplings in NMR-driven protein docking: application to Lys48-linked di-ubiquitin and validation against 15N-relaxation data. Proteins 60, 367-381
10. Cunningham, B. C., Jhurani, P., Ng, P., and Wells, J. A. (1989) Receptor and antibody epitopes in human growth hormone identified by homologscanning mutagenesis. Science 243, 1330-1336
11. Peters, K., and Richards, F. M. (1977) Chemical cross-linking: reagents and problems in studies of membrane structure. Annu. Rev. Biochem. 46, 523-551
12. Janin, J., Henrick, K., Moult, J., Eyck, L. T., Sternberg, M. J., Vajda, S., Vakser, I., and Wodak, S. J. (2003) CAPRI: a Critical Assessment of PRedicted Interactions. Proteins 52, 2-9
13. Méndez, R., Leplae, R., De Maria, L., and Wodak, S. J. (2003) Assessment of blind predictions of protein-protein interactions: current status of docking methods. Proteins 52, 51-67
14. Katchalski-Katzir, E., Shariv, I., Eisenstein, M., Friesem, A. A., Aflalo, C., and Vakser, I. A. (1992) Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques. Proc. Natl. Acad. Sci. U.S.A. 89, 2195-2199
15. Ben-Zeev, E., and Eisenstein, M. (2003) Weighted geometric docking: incorporating external information in the rotation-translation scan. Proteins 52, 24-27
16. Zacharias, M. (2003) Protein-protein docking with a reduced protein model accounting for side-chain flexibility. Protein Sci. 12, 1271-1282
17. Zacharias, M. (2004) Rapid protein-ligand docking using soft modes from molecular dynamics simulations to account for protein deformability: binding of FK506 to FKBP. Proteins 54, 759-767
18. Chen, R., Li, L., and Weng, Z. (2003) ZDOCK: an initial-stage protein-docking algorithm. Proteins 52, 80-87
19. Pierce, B., and Weng, Z. (2007) ZRANK: reranking protein docking predictions with an optimized energy function. Proteins 67, 1078-1086
20. Schneidman-Duhovny, D., Inbar, Y., Nussinov, R., and Wolfson, H. J. (2005) PatchDock and SymmDock: servers for rigid and symmetric docking. Nucleic Acids Res. 33, W363-W367
21. Schneidman-Duhovny, D., Inbar, Y., Polak, V., Shatsky, M., Halperin, I., Benyamini, H., Barzilai, A., Dror, O., Haspel, N., Nussinov, R., and Wolfson, H. J. (2003) Taking geometry to its edge: fast unbound rigid (and hinge-bent) docking. Proteins 52, 107-112
22. Grosdidier, S., Pons, C., Solernou, A., and Fernández-Recio, J. (2007) Prediction and scoring of docking poses with pyDock. Proteins 69, 852-858
23. Cheng, T. M., Blundell, T. L., and Fernandez-Recio, J. (2007) pyDock: electrostatics and desolvation for effective scoring of rigid-body protein-protein docking. Proteins 68, 503-515
24. Gerega, S. K., and Downard, K. M. (2006) PROXIMO - a new docking algorithm to model protein complexes using data from radical probe mass spectrometry (RP-MS). Bioinformatics 22, 1702-1709
25. Lasker, K., Topf, M., Sali, A., and Wolfson, H. J. (2009) Inferential optimization for simultaneous fitting of multiple components into a cryoEM map of their assembly. J. Mol. Biol. 388, 180-194
26. de Vries, S. J., van Dijk, A. D., Krzeminski, M., van Dijk, M., Thureau, A., Hsu, V., Wassenaar, T., and Bonvin, A. M. (2007) HADDOCK versus HADDOCK: new features and performance of HADDOCK2.0 on the CAPRI targets. Proteins 69, 726-733
27. De Vries, S. J., Van Dijk, M., and Bonvin, A. M. (2010) The HADDOCK web server for data-driven biomolecular docking. Nat. Protoc. 5, 883-897
28. Dominguez, C., Boelens, R., and Bonvin, A. M. J. J. (2003) HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. J. Am. Chem. Soc. 125, 1731-1737
29. Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N., and Bourne, P. E. (2000) The Protein Data Bank. Nucleic Acids Res. 28, 235-242
30. Ratnaparkhi, G. S., and Varadarajan, R. (2001) Osmolytes stabilize ribonuclease S by stabilizing its fragments S protein and S peptide to compact folding-competent states. J. Biol. Chem. 276, 28789-28798
31. Berchanski, A., and Eisenstein, M. (2003) Construction of molecular assemblies via docking: modeling of tetramers with D2 symmetry. Proteins 53, 817-829
32. Berchanski, A., Segal, D., and Eisenstein, M. (2005) Modeling oligomers with Cn or Dn symmetry: application to CAPRI target 10. Proteins 60, 202-206
33. Comeau, S. R., and Camacho, C. J. (2005) Predicting oligomeric assemblies: N-mers a primer. J. Struct. Biol. 150, 233-244
34. André, I., Bradley, P., Wang, C., and Baker, D. (2007) Prediction of the structure of symmetrical protein assemblies. Proc. Natl. Acad. Sci. U.S.A. 104, 17656-17661
35. Pierce, B., Tong, W., and Weng, Z. (2005) M-ZDOCK: a grid-based approach for C-n symmetric multimer docking. Bioinformatics 21, 1472-1478
36. Schneidman-Duhovny, D., Inbar, Y., Nussinov, R., and Wolfson, H. J. (2005) Geometry-based flexible and symmetric protein docking. Proteins 60, 224-231
37. Inbar, Y., Benyamini, H., Nussinov, R., and Wolfson, H. J. (2005) Prediction of multimolecular assemblies by multiple docking. J. Mol. Biol. 349, 435-447 (Pubitemid 40693761)
38. Brünger, A. T., Adams, P. D., Clore, G. M., DeLano, W. L., Gros, P., Grosse-Kunstleve, R. W., Jiang, J. S., Kuszewski, J., Nilges, M., Pannu, N. S., Read, R. J., Rice, L. M., Simonson, T., and Warren, G. L. (1998) Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr. D Biol. Crystallogr. 54, 905-921
39. Fernández-Recio, J., Totrov, M., and Abagyan, R. (2004) Identification of protein-protein interaction sites from docking energy landscapes. J. Mol. Biol. 335, 843-865
40. Brunger, A. T. (1992) X-PLOR. A System for X-Ray Crystallography and NMR, Yale University Press, New Haven, CT 225-231
41. Nilges, M. (1993) A Calculation Strategy for the Structure Determination of Symmetrical Dimers by H-1-Nmr. Proteins 17, 297-309
42. O'Donoghue, S. I., and Nilges, M. (1999) Structure Computation and Dynamics in Protein NMR, Kluwer Academic/Plenum Publishers, New York 138-140
43. van Dijk, A. D., de Vries, S. J., Dominguez, C., Chen, H., Zhou, H. X., and Bonvin, A. M. (2005) Data-driven docking: HADDOCK's adventures in CAPRI. Proteins 60, 232-238
44. Levy, E. D., BoeriErba, E., Robinson, C. V., and Teichmann, S. A. (2008) Assembly reflects evolution of protein complexes. Nature 453, 1262-1265
45. Ruotolo, B. T., Giles, K., Campuzano, I., Sandercock, A. M., Bateman, R. H., and Robinson, C. V. (2005) Evidence for macromolecular protein rings in the absence of bulk water. Science 310, 1658-1661
46. Ruotolo, B. T., Benesch, J. L., Sandercock, A. M., Hyung, S. J., and Robinson, C. V. (2008) Ion mobility-mass spectrometry analysis of large protein complexes. Nat. Protoc. 3, 1139-1152
47. Smith, D. P., Knapman, T. W., Campuzano, I., Malham, R. W., Berryman, J. T., Radford, S. E., and Ashcroft, A. E. (2009) Deciphering drift time measurements from travelling wave ion mobility spectrometry-mass spectrometry studies. Eur. J. Mass Spectrom. 15, 113-130
48. Bernstein, S. L., Dupuis, N. F., Lazo, N. D., Wyttenbach, T., Condron, M. M., Bitan, G., Teplow, D. B., Shea, J. E., Ruotolo, B. T., et al. (2009) Amyloid-beta protein oligomerization and the importance of tetramers and dodecamers in the aetiology of Alzheimer's disease. Nat. Chem. 1, 326-331
49. Walhout, A. J., and Vidal, M. (2001) Protein interaction maps for model organisms. Nat. Rev. Mol. Cell Biol. 2, 55-62
50. Auerbach, D., Fetchko, M., and Stagljar, I. (2003) Proteomic approaches for generating comprehensive protein interaction maps. Targets 2, 85-92
51. Ho, Y., Gruhler, A., Heilbut, A., Bader, G. D., Moore, L., Adams, S. L., Millar, A., Taylor, P., Bennett, K., Boutilier, K., Yang, L., Wolting, C., Donaldson, I., Schandorff, S., Shewnarane, J., Vo, M., Taggart, J., Goudreault, M., Muskat, B., Alfarano, C., Dewar, D., Lin, Z., Michalickova, K., Willems, A. R., Sassi, H., Nielsen, P. A., Rasmussen, K. J., Andersen, J. R., Johansen, L. E., Hansen, L. H., Jespersen, H., Podtelejnikov, A., Nielsen, E., Crawford, J., Poulsen, V., Sørensen, B. D., Matthiesen, J., Hendrickson, R. C., Gleeson, F., Pawson, T., Moran, M. F., Durocher, D., Mann, M., Hogue, C. W., Figeys, D., and Tyers, M. (2002) Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415, 180-183
52. Gavin, A. C., Bösche, M., Krause, R., Grandi, P., Marzioch, M., Bauer, A., Schultz, J., Rick, J. M., Michon, A. M., Cruciat, C. M., Remor, M., Höfert, C., Schelder, M., Brajenovic, M., Ruffner, H., Merino, A., Klein, K., Hudak, M., Dickson, D., Rudi, T., Gnau, V., Bauch, A., Bastuck, S., Huhse, B., Leutwein, C., Heurtier, M. A., Copley, R. R., Edelmann, A., Querfurth, E., Rybin, V., Drewes, G., Raida, M., Bouwmeester, T., Bork, P., Seraphin, B., Kuster, B., Neubauer, G., and Superti-Furga, G. (2002) Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415, 141-147
53. 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., and Rothberg, J. M. (2000) A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403, 623-627 (Pubitemid 30103994)
54. Ito, T., Chiba, T., Ozawa, R., Yoshida, M., Hattori, M., and Sakaki, Y. (2001) A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl. Acad. Sci. U.S.A. 98, 4569-4574
55. Yu, H., Braun, P., Yildirim, M. A., Lemmens, I., Venkatesan, K., Sahalie, J., Hirozane-Kishikawa, T., Gebreab, F., Li, N., Simonis, N., Hao, T., Rual, J. F., Dricot, A., Vazquez, A., Murray, R. R., Simon, C., Tardivo, L., Tam, S., Svrzikapa, N., Fan, C., de Smet, A. S., Motyl, A., Hudson, M. E., Park, J., Xin, X., Cusick, M. E., Moore, T., Boone, C., Snyder, M., Roth, F. P., Barabási, A. L., Tavernier, J., Hill, D. E., and Vidal, M. (2008) High-quality binary protein interaction map of the yeast interactome network. Science 322, 104-110
56. Tarassov, K., Messier, V., Landry, C. R., Radinovic, S., Serna Molina, M. M., Shames, I., Malitskaya, Y., Vogel, J., Bussey, H., and Michnick, S. W. (2008) An in vivo map of the yeast protein interactome. Science 320, 1465-1470
57. Zhu, H., Bilgin, M., Bangham, R., Hall, D., Casamayor, A., Bertone, P., Lan, N., Jansen, R., Bidlingmaier, S., Houfek, T., Mitchell, T., Miller, P., Dean, R. A., Gerstein, M., and Snyder, M. (2001) Global analysis of protein activities using proteome chips. Science 293, 2101-2105
58. Hart, G. T., Ramani, A. K., and Marcotte, E. M. (2006) How complete are current yeast and human protein-interaction networks? Genome Biol. 7, 120.1-120.9
59. von Mering, C., Krause, R., Snel, B., Cornell, M., Oliver, S. G., Fields, S., and Bork, P. (2002) Comparative assessment of large-scale data sets of protein-protein interactions. Nature 417, 399-403
60. Gavin, A. C., Aloy, P., Grandi, P., Krause, R., Boesche, M., Marzioch, M., Rau, C., Jensen, L. J., Bastuck, S., Dümpelfeld, B., Edelmann, A., Heurtier, M. A., Hoffman, V., Hoefert, C., Klein, K., Hudak, M., Michon, A. M., Schelder, M., Schirle, M., Remor, M., Rudi, T., Hooper, S., Bauer, A., Bouwmeester, T., Casari, G., Drewes, G., Neubauer, G., Rick, J. M., Kuster, B., Bork, P., Russell, R. B., and Superti-Furga, G. (2006) Proteome survey reveals modularity of the yeast cell machinery. Nature 440, 631-636
61. Goll, J., and Uetz, P. (2006) The elusive yeast interactome. Genome Biol. 7, 223.1-223.6
62. Kastritis, P. L., and Bonvin, A. M. J. J. (2010) Are scoring functions in protein protein docking ready to predict interactomes? Clues from a novel binding affinity benchmark. J. Proteome Res., in press
63. Fernandez-Ballester, G., and Serrano, L. (2006) Prediction of protein-protein interaction based on structure. Methods Mol. Biol. 340, 207-234
64. Tong, A. H., Drees, B., Nardelli, G., Bader, G. D., Brannetti, B., Castagnoli, L., Evangelista, M., Ferracuti, S., Nelson, B., Paoluzi, S., Quondam, M., Zucconi, A., Hogue, C. W., Fields, S., Boone, C., and Cesareni, G. (2002) A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules. Science 295, 321-324
65. Hennig, J., Hennig, K. D., and Sunnerhagen, M. (2008) MTMDAT: automated analysis and visualization of mass spectrometry data for tertiary and quaternary structure probing of proteins. Bioinformatics 24, 1310-1312
66. Volz, K. (1999) A test case for structure-based functional assignment: the 1.2 angstrom crystal structure of the yjgF gene product from Escherichia coli. Protein Sci. 8, 2428-2437
67. Bressanelli, S., Stiasny, K., Allison, S. L., Stura, E. A., Duquerroy, S., Lescar, J., Heinz, F. X., and Rey, F. A. (2004) Structure of a flavivirus envelope glycoprotein in its low-pH-induced membrane fusion conformation. EMBO J. 23, 728-738
68. Loris, R., Tielker, D., Jaeger, K. E., and Wyns, L. (2003) Structural basis of carbohydrate recognition by the lectin LecB from Pseudomonas aeruginosa. J. Mol. Biol. 331, 861-870
69. Badger, J., Sauder, J. M., Adams, J. M., Antonysamy, S., Bain, K., Bergseid, M. G., Buchanan, S. G., Buchanan, M. D., Batiyenko, Y., Christopher, J. A., Emtage, S., Eroshkina, A., Feil, I., Furlong, E. B., Gajiwala, K. S., Gao, X., He, D., Hendle, J., Huber, A., Hoda, K., Kearins, P., Kissinger, C., Laubert, B., Lewis, H. A., Lin, J., Loomis, K., Lorimer, D., Louie, G., Maletic, M., Marsh, C. D., Miller, I., Molinari, J., Muller-Dieckmann, H. J., Newman, J. M., Noland, B. W., Pagarigan, B., Park, F., Peat, T. S., Post, K. W., Radojicic, S., Ramos, A., Romero, R., Rutter, M. E., Sanderson, W. E., Schwinn, K. D., Tresser, J., Winhoven, J., Wright, T. A., Wu, L., Xu, J., and Harris, T. J. (2005) Structural analysis of a set of proteins resulting from a bacterial genomics project. Proteins 60, 787-796
70. Stehle, T., and Harrison, S. C. (1997) High-resolution structure of a polyomavirus VP1-oligosaccharide complex: implications for assembly and receptor binding. EMBO J. 16, 5139-5148
71. Mondragón, A., and Harrison, S. C. (1991) The phage-434 Cro/Or1 complex at 2.5Å resolution. J. Mol. Biol. 219, 321-334