Identifying putative drug targets and potential drug leads: Starting points for virtual screening and docking

Methods in Molecular Biology

Volumn 443, Issue , 2008, Pages 333-351

  Wishart, David S ^a  

^a UNIVERSITY OF ALBERTA   (Canada)

Author keywords

Bioinformatics; Chemical similarity; Disease; Drug; Drug target; Endogenous disease; Exogenous disease; Metabolite; Sequence comparison

Indexed keywords

BACTERIA (MICROORGANISMS);

EID: 84934440060     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-59745-177-2_17     Document Type: Article

References (30)

1. Geldenhuys, W.J., Gaasch, K.E., Watson, M., Allen, D.D., and Van der Schyf, C.J. (2006) Optimizing the use of open-source software applications in drug discovery. Drug Discov. Today. 11, 127-132.
2. Kirkpatrick, D.L., Watson, S., and Ulhaq, S. (1999) Structure-based drug design: combinatorial chemistry and molecular modeling. Comb. Chem. High Throughput Screen. 2, 211-221.
3. Fiser, A. and Sali, A. (2003) Modeller: generation and refinement of homology-based protein structure models. Methods Enzymol. 374, 461-491.
4. Mohan, V., Gibbs, A.C., Cummings, M.D., Jaeger, E.P., and DesJarlais, R.L. (2005) Docking: successes and challenges. Curr. Pharm. Des. 11, 323-333.
5. Jain, A.N. (2004) Virtual screening in lead discovery and optimization. Curr. Opin. Drug Discov. Devel. 7, 396-403.
6. Alvarez, J.C. (2004) High-throughput docking as a source of novel drug leads. Curr. Opin. Chem. Biol. 8, 365-370.
7. Taylor, R.D., Jewsbury, P.J., and Essex, J.W. (2002) A review of protein-small molecule docking methods. J. Comput. Aided Mol. Des. 16, 151-166.
8. Shoichet, B.K. and Kuntz, I.D. (1993) Matching chemistry and shape in molecular docking. Protein Eng. 6, 723-732.
9. Goodsell, D.S., Morris, G.M., and Olson, A.J. (1996) Automated docking of flexible ligands: applications of AutoDock. J. Mol. Recognit. 9, 1-5.
10. Jones, G., Willett, P., Glen, R.C., Leach, A.R., and Taylor, R. (1997) Development and validation of a genetic algorithm for flexible docking. J. Mol. Biol. 267, 727-748.
11. Friesner, R.A., Banks, J.L., Murphy, R.B., Halgren, T.A., Klicic, J.J., Mainz, D.T., Repasky, M.P., Knoll, E.H., Shelley, M., Perry, J.K., Shaw, D.E., Francis, P., and Shenkin, P.S. (2004) Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J. Med. Chem. 47, 1739-1749.
12. Wishart, D.S., Knox, C., Guo, A.C., Shrivastava, S., Hassanali, M., Stothard, P., Chang, Z., and Woolsey, J. (2006) DrugBank: a comprehensive resource for in silico drug discovery and exploration. Nucleic Acids Res. 34(Database issue):D668-672.
13. Wheeler, D.L., Barrett, T., Benson, D.A., Bryant, S.H., Canese, K., Chetvernin, V., Church, D.M., DiCuccio, M., Edgar, R., Federhen, S., Geer, L.Y., Helmberg, W., Kapustin, Y., Kenton, D.L., Khovayko, O., Lipman, D.J., Madden, T.L., Maglott, D.R., Ostell, J., Pruitt, K.D., Schuler, G.D., Schriml, L.M., Sequeira, E., Sherry, S.T., Sirotkin, K., Souvorov, A., Starchenko, G., Suzek, T.O., Tatusov, R., Tatusova, T.A., Wagner, L., and Yaschenko, E. (2006) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 34(Database issue):D173-180.
14. Wishart, D.S., Metabolism and Metabolic Disease Resources on the Web, Chapter3.1 (2006) in, The Metabolic and Molecular Bases of Inherited Disease - OMMBID (Scriver, C.R., Beaudet, A.L., Sly, W.S., Valle, D., Vogelstein, B. eds), McGraw-Hill, New York. www.ommbid.com
15. Sweetman, S. (2004) Martindale: The Complete Drug Reference, 34th edition, Pharmaceutical Press, New York, NY
16. Krogh, A., Larsson, B., von Heijne, G., and Sonnhammer, E.L. (2001) Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol. 305, 567-580.
17. Gardy, J.L., Laird, M.R., Chen, F., Rey, S., Walsh, C.J., Ester, M., and Brinkman, F.S. (2005) PSORTb v.2.0: expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis. Bioinformatics. 21, 617-623.
18. Zhang, R., Ou, H.Y., and Zhang, C.T. (2004) DEG: a database of essential genes. Nucleic Acids Res. 32(Database issue):D271-272.
19. Ihlenfeldt, W.D., Voigt, J.H., Bienfait, B., Oellien, F., and Nicklaus, M.C. (2002) Enhanced CACTVS browser of the Open NCI Database. J. Chem. Inf. Comput. Sci. 42, 46-57.
20. Hamosh, A., Scott, A.F., Amberger, J.S., Bocchini, C.A., and McKusick, V.A. (2005) Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res. 33(Database issue), D514-517.
21. Darvasi, A. (2005) Dissecting complex traits: the geneticists' "Around the world in 80 days". Trends Genet. 21, 373-376.
22. Clarke, P.A., te Poele, R., and Workman, P. (2004) Gene expression microarray technologies in the development of new therapeutic agents. Eur. J. Cancer. 40, 2560-2591.
23. Rebhan, M., Chalifa-Caspi, V., Prilusky, J., and Lancet, D. (1998) GeneCards: a novel functional genomics compendium with automated data mining and query reformulation support. Bioinformatics. 14, 656-664.
24. Hu, Y., Hines, L.M., Weng, H., Zuo, D., Rivera, M., Richardson, A., and LaBaer, J. (2003) Analysis of genomic and proteomic data using advanced literature mining. J. Proteome Res. 2, 405-412.
25. Wishart, D.S. (2005) Bioinformatics in drug development and assessment. Drug Metab. Rev. 37, 279-310.
26. Hopkins, A.L. and Groom, C.R. (2002) The druggable genome Nat. Rev. Drug Discov. 1, 727-730.
27. Needleman, S.B. and Wunsch, C.D. (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 48, 443-453.
28. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402.
29. Weininger, D. (1988) SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules. J. Chem. Inf. Comput. Sci. 28, 31-36.
30. Ullman, J.R. (1976) An algorithm for sub-graph isomorphism, J. ACM 23, 31-42.