Bibliography for the Drug Target Identification from Microbial Genomes


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Bibliography for the Drug Target Identification from Microbial Genomes

  1. 1. Bibliography _________________________________________________________________________ Identification and Validation of Drug Targets 153 BIBLIOGRAPHY . . Adams, G. (2000). Lecture Notes, Microbiology, 29 Feb. 2000. Akerley, B. J., Rubin, E. J., Camilli, A., Lampe, D. J., Robertson, H. M. and Mekalanos, J. J. (1998). Systematic identification of essential genes by in vitro mariner mutagenesis. Proc. Natl. Acad. Sci. USA., 95, 8927-8932. Altschul S. F. (1990). Basic local alignment search tool. J. Mol. Biol., 215, 403- 410. Anderson, A. A. (2003). Chemistry and Biology, 10, 787. Aradi, I. and Erdi, P. (2006). Computational neuropharmacology, dynamical approaches in drug discovery. Trends Pharmacol. Sci., 27, 240-243. Arigoni, F., Talabot, F., Peitsch, M., Edgerton, M. D., Meldrum, E., Allet, E., Fish, R., Jamotte, T., Curchod, M. L. and Loferer, H. (1998). A genome-based approach for the identification of essential bacterial genes. Nat. Biotechnol., 16, 851-856. Aronov, A. M., Balakin, K. V., Kiselyov, A., Varma-O’Brien, S. and Ekins, S. (2006). Applications of QSAR methods to ion channels. In, Ekins S (ed). Computational Toxicology, Risk Assessment for Pharmaceutical and Environmental Chemicals. John Wiley and Sons, Hoboken, NJ.
  2. 2. Bibliography _________________________________________________________________________ Identification and Validation of Drug Targets 154 Auckland, C., Teare, L., Cooke, F., Kaufmann, M. E., Warner, M., Jones, G., Bamford, K., Ayles, H., Johnson, A. P. (2002). J. Antimicrob. Chemother. , 50, 743−746. Badarinarayana, V., Estep, P. W., Shendure, J., Edwards, J., Tavazoie, S., Lam, F. and Church, G. M. (2001). Selection analyses of insertional mutants using subgenic-resolution arrays. Nat. Biotechnol., 19, 1060-1065. Bairoch, A., Apweiler, R., Wu, C. H., Barker, W. C., Boeckmann, B., Ferro, S., Gasteiger, E., Huang, H., Lopez, R. and Magrane, M. (2005). The Universal Protein Resource (UniProt). Nucleic Acids Res., 33, D154–D159. Bajorath, J. (2002). Nat. Rev. Drug Discov., 1, 882-894. Barbachyn, M. R., Brickner, S. J., Gadwood, R. C., Garmon, S. A., Grega, K. C., Hutchinson, D. K., Munesada, K., Reischer, R. J., Taniguchi, M., Thomasco, L. M., Toops, D. S., Yamada, H., Ford, C. W., and Zurenko, G. E. (1998). Adv. Exp. Med. Biol., 456, 219−238. Bartel, P. (1993). Elimination of false positives that arise in using the two-hybrid system. Biotechniques, 14, 920-924. Becker, O. M., Shacham, S., Marantz, Y. and Noiman, S. (2003). Curr. Opin. Drug Discov. Devel. , 6, 353-361. Becker, O. M., Shacham, S., Topf, M. and Naor, Z. (2000). World Patent, WO- 02_15106-A2.
  3. 3. Bibliography _________________________________________________________________________ Identification and Validation of Drug Targets 155 Beddell, C. R. (1976). Br. J. Pharmacol., 57, 201. [PMID, 938794]. Behr, M. A. (1999). Comparative genomics of BCG vaccines by whole-genome DNA microarray. Science, 284, 1520-1523. Benton, B. L., J. Ving, F. Malouin, P. K. Martin, M. B. Schmid, and D. Sun. March (2000). Methods of screening for compounds active on Staphylococcus aureus target genes. US Patent, 6, 37-123. Benton, B. L., J. Ving, F. Malouin, P. K. Martin, M. B. Schmid, and D. Sun. (2001). Methods of screening for compounds active on Staphylococcus aureus target genes. US Patent, 6, 228, 588. Berg, C. M. and Berg, D. A. (1996). Transposable element tools for microbial genetics. In: Escherichia coli and Salmonella (Neidhardt F. C. ed. ), pp. 2588-2612. Bernal, A., Ear, U. and Kyrpides N. (2001). Genomes OnLine Database (GOLD), a monitor of genome projects world-wide. Nucleic Acids Res. , 29, 126-127. Bernstein, F. C., Koetzle, T. F., Williams, T. F., Meyer, G. J. B., Jr, Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T. and Tasumi, M. (1977). The Protein Data Bank, A computer-based archival file for macromolecular structures. J. Mol. Biol., 112, 535–542.
  4. 4. Bibliography _________________________________________________________________________ Identification and Validation of Drug Targets 156 Bissantz, C., Bernard, P., Hibert, M. and Rognan, D. (2003). Protein-based virtual screening of chemical databases. II. Are homology models of G-protein coupled receptors suitable targets? Proteins, 50, 5-25. Blattner, F. R. (1997). The complete genome sequence of Escherichia coli K-12. Science, 277, 1453-1462. Block, P., Sotriffer, C. A., Dramburg, I. and Klebe, G. (2006). AffinDB, Afreely accessible database of affinities for protein–ligand complexes from the PDB. Nucleic Acids Res., 34, D522–D526. Blundell, T. L. (1972). Adv. Protein Chem., 26, 279. Blundell, T. L. (1996). Nature, 384, 23. [PMID, 8895597]. Bonacci, T. M., Mathews, J. L., Yuan, C., Lehmann, D. M., Malik, S. and Wu, D. (2006). Differential targeting of Gbetagamma-subunit signaling with small molecules. Science, 312, 443-446. Brewerton, S. C., Dore, A. S., Drake, A. C., Leuther, K. K. and Blundell, T. L. (2004). Structural analysis of DNA-PKcs, modelling of the repeat units and insights into the detailed molecular architecture. J. Struct. Biol., 145, 295-306. C. R. Beddell (1976), Br. J. Pharmacol., 57, 201 (1976). [PMID, 938794]. Cacace, A. (2003). Drug Discovery Today, 8, 785. [PMID, 12946641] Campbell, S. F. (2000). Clin. Sci., 99, 255. [PMID, 10995589].
  5. 5. Bibliography _________________________________________________________________________ Identification and Validation of Drug Targets 157 Carper, S. W., Duffy, J. J. and Gerner, E. W. (1987). Cancer Res., 47, 5249-5255. Cassell, G. H. and Mekalanos, J. (2001). JAMA, 285, 601−605. Chalker, A. F., Minehart, H. W., Hughes, N. J., Koretke, K. K., Lonetto, M. A., Brinkman, K. K., Warren, P. V., Lupas, A., Stanhope, M. J., Brown, J. R. and Hoffman, P. S. (2001). Systematic identification of selective essential genes in Helicobacter pylori by genome prioritization and allelic replacement mutagenesis. J. Bacteriol. , 183, 1259-1268. Chang, C. and Swaan, P. W. (2005). Computational approaches to modeling drug transporters. Eur. J. Pharm. Sci., 27, 411-424. Chang, C., Bahadduri, P. M., Polli, J. E., Swaan, P. W. and Ekins, S. (2006a). Rapid identification of P-glycoprotein substrates and inhibitors. Drug Metab. Dispos., 34, 1976-1984. Chang, C., Ekins, S., Bahadduri, P. and Swaan, P. W. (2006b). Pharmacophorebased discovery of ligands for drug transporters. Adv. Drug Del. Rev., 58, 1431-1450. Chen, Y. Z. and Ung, C. Y. (2001). Prediction of potential toxicity and side effect protein targets of a small molecule by a ligand-protein inverse docking approach. J. Mol. Graph. Model., 20, 199-218.
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  7. 7. Bibliography _________________________________________________________________________ Identification and Validation of Drug Targets 159 Dajani, R., Cleasby, A., Neu, M., Wonacott, A. J., Jhoti, H. and Hood, A. M. (1999). X-ray crystal structure of human dopamine sulfotransferase, SULT1A3. J. Biol. Chem., 53, 37862-37868. Danchin, A., Medigue, C., Gascuel, O., Soldano, H. and Henaut, A. (1991). From data banks to data bases. Res. Microbiol., 142, 913-916. Davie, E. W. (1991). Biochemistry, 30, 10363. [PMID, 1931959]. Davie, E. W. (1991). Biochemistry, 30, 10363. [PMID, 1931959]. Davis, A. M. (2003). Angew. Chem. Int. Ed., 42, 2718. [PMID, 12820253]. De Graaf, C., Vermeulen, N. P. and Feenstra, K. A. (2005). Cytochrome P450 in silico, an integrative modeling approach. J. Med. Chem., 48, 2725-2755. De Groot, M. J. and Ekins, S. (2002). Pharmacophore modeling of cytochromes P450. Adv. Drug. Del. Rev., 54, 367-383. De, Groot, M. J. (2006). Designing better drugs, predicting cytochrome P450 metabolism. Drug Discov. Today, 11, 601-606. Deisenhofer, J. and Smith, J. L. (2001). Curr. Opin. Struc. Bio., 11, 701. Demple, B., Sedgwick, B., Robins, P., Totty, N., Waterfield, M. D. and Lindahl, T. (1985). Proc. Natl. Acad. Sci. U. S. A., 82, 2688-2692. Di Masi, J. A. (2002). The value of improving the productivity of the drug development process. Pharmacoeconomics, 20 (Suppl. 3), 1-10.
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