A synopsis of some of the approaches to protein target selection is given, with an emphasis on using web resources to converge on well-ordered, readily crystallizable proteins that are maximally different from known structures. This is illustrated with the genomes of the pathogens causing tuberculosis and sleeping sickness.
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Dale, G. E., Oefner, C., and D'Arcy, A. (2003) J. Struct. Biol. 142, 88–97.
Cole, S. T., Brosch, R., Parkhill, J., Garnier, T., Churcher, C., Harris, D., Gordon, S. V., Eiglmeier, K., Gas, S., Barry, C. E., III, Tekaia, F., Badcock, K., Basham, D., Brown, D., Chillingworth, T., Connor, R., Davies, R., Devlin, K., Feltwell, T., Gentles, S., Hamlin, N., Holroyd, S., Hornsby, T., Jagels, K., Krogh, A., McLean, J., Moule, S., Murphy, L., Oliver, K., Osborne, J., Quail, M. A., Rajandream, M. A., Rogers, J., Rutter, S., Seeger, K., Skelton, J., Squares, R., Squares, S., Sulston, J. E., Taylor, K., Whitehead, S., and Barrell, B. G. (1998) Nature 393, 537–544.
Cole, S. T., Eiglmeier, K., Parkhill, J., James, K. D., Thomson, N. R., Wheeler, P. R., Honore, N., Garnier, T., Churcher, C., Harris, D., Mungall, K., Basham, D., Brown, D., Chillingworth, T., Connor, R., Davies, R. M., Devlin, K., Duthoy, S., Feltwell, T., Fraser, A., Hamlin, N., Holroyd, S., Hornsby, T., Jagels, K., Lacroix, C., Maclean, J., Moule, S., Murphy, L., Oliver, K., Quail, M. A., Rajandream, M. A., Rutherford, K. M., Rutter, S., Seeger, K., Simon, S., Simmonds, M., Skelton, J., Squares, R., Squares, S., Stevens, K., Taylor, K., Whitehead, S., Woodward, J. R., and Barrell, B. G. (2001) Nature 409, 1007–11.
El-Sayed, N. M., Myler, P. J., Blandin, G., Berriman, M., Crabtree, J., Aggarwal, G., Caler, E., Renauld, H., Worthey, E. A., Hertz-Fowler, C., Ghedin, E., Peacock, C., Bartholomeu, D. C., Haas, B. J., Tran, A.-N., Wortman, J. R., Alsmark, U. C. M., Angiuoli, S., Anupama, A., Badger, J., Bringaud, F., Cadag, E., Carlton, J. M., Cerqueira, G. C., Creasy, T., Delcher, A. L., Djikeng, A., Embley, T. M., Hauser, C., Ivens, A. C., Kummerfeld, S. K., Pereira-Leal, J. B., Nilsson, D., Peterson, J., Salzberg, S. L., Shallom, J., Silva, J. C., Sundaram, J., Westenberger, S., White, O., Melville, S. E., Donelson, J. E., Andersson, B., Stuart, K. D., and Hall, N. (2005) Science 309, 404–409.
Aksoy, S., O'Neill, S. L., Maudlin, I., Dale, C., and Robinson, A. S. (2001) Trends Parasitol. 17, 29–35.
Meyer, A., and Peer, Y. V. d. (2005) BioEssays 27, 937–945.
Cottage, A. J., Edwards, Y. J. K., and Elgar, G. (2003) Mammal. Gen. 14, 514–525.
Marcotte, E. M., Pellegrini, M., Ng, H.-L., Rice, D. W., Yeates, T. O., and Eisenberg, D. (1999) Science 285, 751–753.
Marcotte, E. M., Xenarios, I., van der Bliek, A. M., and Eisenberg, D. (2000) PNAS 97, 12115–12120.
Pollard, K. S., Salama, S. R., Lambert, N., Lambot, M.-A., Coppens, S., Pedersen, J. S., Katzman, S., King, B., Onodera, C., Siepel, A., Kern, A. D., Dehay, C., Igel, H., Ares, M., Vanderhaeghen, P., and Haussler, D. (2006) Nature 443, 167–172.
Tatusov, R. L., Koonin, E. V., and Lipman, D. J. (1997) Science 278, 631–637.
Albert, R., and Barabási, A.-L. (2002) Rev. Mod. Phys. 74, 47.
Jeong, H., Mason, S. P., Barabasi, A. L., and Oltvai, Z. N. (2001) Nature 411, 41–42.
Eisenberg, D., Marcotte, E. M., Xenarios, I., and Yeates, T. O. (2000) Nature 405, 823–826.
Lee, I., Date, S. V., Adai, A. T., and Marcotte, E. M. (2004) Science 306, 1555–1558.
Sprinzak, E., Altuvia, Y., and Margalit, H. (2006) PNAS 103, 14718–14723.
Shoemaker, B. A., Panchenko, A. R., and Bryant, S. H. (2006) Protein Sci. 15, 352–361.
Flannick, J., Novak, A., Srinivasan, B. S., McAdams, H. H., and Batzoglou, S. (2006) Genome Res. 16, 1169–1181.
Quackenbush, J. (2003) Science 302, 240–241.
Uetz, P., and Pankratz, M. J. (2004) Nat. Biotech. 22, 43–44.
Aloy, P., and Russell, R. B. (2004) Nat. Biotech. 22, 1317–1321.
Kitano, H. (2002) Science 295, 1662.
Salwinski, L., Miller, C. S., Smith, A. J., Pettit, F. K., Bowie, J. U., and Eisenberg, D. (2004) Nucl. Acids Res. 32, D449–451.
Derewenda, Z. S. (2004) Structure 12, 529–535.
Kendrew, J. C., Parrish, R. G., Marrack, J. R., and Orlans, E. S. (1954) Nature 174, 946–949.
Fink, A. L. (2005) Curr. Opin. Struct. Biol. 15, 35–41.
Uversky, V. N., Gillespie, J. R., and Fink, A. L. (2000) Prot. Struct. Funct. Genet. 41, 415–427.
Prilusky, J., Felder, C. E., Zeev-Ben-Mordehai, T., Rydberg, E. H., Man, O., Beckmann, J. S., Silman, I., and Sussman, J. L. (2005) Bioinformatics 21, 3435–3438.
Yang, Z. R., Thomson, R., McNeil, P., and Esnouf, R. M. (2005) Bioinformatics 21, 3369–3376.
Altschul, S. F., Gish, W., Miller, W., Meyers, E. W., and Lipman, D. J. (1990) J. Mol. Biol. 215, 403–410.
Kifer, I., Sasson, O., and Linial, M. (2005) Bioinformatics 21, 1020–1027.
Chandonia, J.-M., and Brenner, S. E. (2005) Prot. Struct. Funct. Bioinformat. 58, 166–179.
Geer, L. Y., Domrachev, M., Lipman, D. J., and Bryant, S. H. (2002) Genome Res. 12, 1619–1623.
Mallick, P., Weiss, R., and Eisenberg, D. (2002) PNAS 99, 16041–16046.
Fischer, D., and Eisenberg, D. (1996) Prot. Sci. 5, 947–955.
Carter, J. C. W., and Duax, W. L. (2002) Mol. Cell 10, 705–708.
Johnson, Z. I., and Chisholm, S. W. (2004) Genome Res. 14, 2268–2272.
Krogh, A., Larsson, B., von Heijne, G., and Sonnhammer, E. L. L. (2001) J. Mol. Biol. 305, 567–580.
Stajich, J. E., Block, D., Boulez, K., Brenner, S. E., Chervitz, S. A., Dagdigian, C., Fuellen, G., Gilbert, J. G. R., Korf, I., Lapp, H., Lehvaslaiho, H., Matsalla, C., Mungall, C. J., Osborne, B. I., Pocock, M. R., Schattner, P., Senger, M., Stein, L. D., Stupka, E., Wilkinson, M. D., and Birney, E. (2002) Genome Res. 12, 1611–1618.
Collaborative (1994) Acta Crystallogr. Sect. D 50, 760–763.
Raftery, J., and Helliwell, J. R. (2002) Acta Crystallogr. Sect. D 58, 875–877.
Fraser, C. M., Gocayne, J. D., White, O., Adams, M. D., Clayton, R. A., Fleischmann, R. D., Bult, C. J., Kerlavage, A. R., Sutton, G., Kelley, J. M., Fritchman, J. L., Weidman, J. F., Small, K. V., Sandusky, M., Fuhrmann, J., Nguyen, D., Utterback, T. R., Saudek, D. M., Phillips, C. A., Merrick, J. M., Tomb, J.-F., Dougherty, B. A., Bott, K. F., Hu, P.-C., and Lucier, T. S. (1995) Science 270, 397–404.
Koonin, E. V. (2003) Nat. Rev. Microbiol. 1, 127–136.
Rio, R. V. M., Hu, Y., and Aksoy, S. (2004) Trends Microbiol. 12, 325–336.
Zientz, E., Dandekar, T., and Gross, R. (2004) Microbiol. Mol. Biol. Rev. 68, 745–770.
Acknowledgments
The author thanks John R. Helliwell for detailed discussions. This chapter is a contribution to the UK North West Structural Genomics Consortium (NWSGC) coordinated by S. S. Hasnain, CCLRC Daresbury Laboratory, UK.
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Raftery, J. (2008). Target Selection: Triage in the Structural Genomics Battlefield. In: Kobe, B., Guss, M., Huber, T. (eds) Structural Proteomics. Methods in Molecular Biology™, vol 426. Humana Press. https://doi.org/10.1007/978-1-60327-058-8_3
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