Informatics resources for tuberculosis - Towards drug discovery

Tuberculosis

Volumn 92, Issue 2, 2012, Pages 133-138

  Sundaramurthi, Jagadish Chandrabose ^a   Brindha, S ^b   Reddy, T B K ^c   Hanna, Luke Elizabeth ^a  

^a NATIONAL INSTITUTE FOR RESEARCH IN TUBERCULOSIS   (India)

^b UNIVERSITY OF MADRAS   (India)

^c STANFORD UNIVERSITY   (United States)

Author keywords

Bioinformatics; Cheminformatics; Database; Drug discovery; Tuberculosis

Indexed keywords

BACTERIAL GENOME; BIOINFORMATICS; DRUG TARGETING; GENE EXPRESSION; GENE REGULATORY NETWORK; GENETIC DATABASE; GENOMICS; HUMAN; METABOLISM; MULTIDRUG RESISTANT TUBERCULOSIS; MYCOBACTERIUM AVIUM; MYCOBACTERIUM BOVIS; MYCOBACTERIUM LEPRAE; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; OPERON; PRIORITY JOURNAL; REVIEW; TUBERCULOSIS;

ANTITUBERCULAR AGENTS; COMPUTATIONAL BIOLOGY; DATABASES, FACTUAL; DRUG DISCOVERY; DRUG RESISTANCE, MULTIPLE, BACTERIAL; GENE REGULATORY NETWORKS; GENOMICS; HUMANS; MYCOBACTERIUM TUBERCULOSIS;

EID: 84857368197     PISSN: 14729792     EISSN: 1873281X     Source Type: Journal    
DOI: 10.1016/j.tube.2011.08.006     Document Type: Review

References (47)

1. S.T. Cole, R. Brosch, J. Parkhill, T. Garnier, C. Churcher, and D. Harris Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence Nature 393 1998 537 544
2. E.C. Rivers, and R.L. Mancera New anti-tuberculosis drugs in clinical trials with novel mechanisms of action Drug Discov Today 13 2008 1090 1098
3. J.M. Lew, A. Kapopoulou, L.M. Jones, and S.T. Cole TubercuList - 10 years after Tuberculosis (Edinb) 91 2011 1 7
4. P.E. Jacques, A.L. Gervais, M. Cantin, J.F. Lucier, G. Dallaire, and G. Drouin MtbRegList, a database dedicated to the analysis of transcriptional regulation in Mycobacterium tuberculosis Bioinformatics 21 2005 2563 2565
5. S. Ranjan, R.K. Gundu, and A. Ranjan MycoperonDB: a database of computationally identified operons and transcriptional units in Mycobacteria BMC Bioinform 7 Suppl 5 2006 18 S9
6. J. Krawczyk, T.A. Kohl, A. Goesmann, J. Kalinowski, and J. Baumbach From Corynebacterium glutamicum to Mycobacterium tuberculosis-towards transfers of gene regulatory networks and integrated data analyses with MycoRegNet Nucleic Acids Res 37 2009 97
7. M. Pertea, K. Ayanbule, M. Smedinghoff, and S.L. Salzberg OperonDB: a comprehensive database of predicted operons in microbial genomes Nucleic Acids Res 37 2009 D479 D482
8. Operon DB. Available from http://operondb.cbcb.umd.edu/cgi-bin/operondb/ operons.cgi [accessed on 03.08.11].
9. S. Okuda, T. Katayama, S. Kawashima, S. Goto, and M. Kanehisa ODB: a database of operons accumulating known operons across multiple genomes Nucleic Acids Res 34 2006 D358 D462
10. F. Mao, P. Dam, J. Chou, V. Olman, and Y. Xu DOOR: a database for prokaryotic operons Nucleic Acids Res 37 2009 D459 D463
11. The database of Conditionally Regulated proteins in Mycobacterium tuberculosis. Available from http://www.doe-mbi.ucla.edu/Services/MTBreg/ [accessed on 4.04.11].
12. P.M. Bowers, M. Pellegrini, M.J. Thompson, J. Fierro, T.O. Yeates, and D. Eisenberg Prolinks: a database of protein functional linkages derived from coevolution Genome Biol 5 2004 R35
13. T.R. Ioerger, and J.C. Sacchettini Structural genomics approach to drug discovery for Mycobacterium tuberculosis Curr Opin Microbiol 12 2009 318 325
14. T.B. Reddy, R. Riley, F. Wymore, P. Montgomery, D. DeCaprio, and R. Engels TB. database: an integrated platform for tuberculosis research Nucleic Acids Res 37 2009 D499 D508
15. J.E. Galagan, P. Sisk, C. Stolte, B. Weiner, M. Koehrsen, and F. Wymore TB database 2010: overview and update Tuberculosis (Edinb) 90 2010 225 235
16. A. Vishnoi, A. Srivastava, R. Roy, and A. Bhattacharya MGDD: Mycobacterium tuberculosis genome divergence database BMC Genomics 9 2008 373
17. M. Catanho, D. Mascarenhas, W. Degrave, and A.B. Miranda GenoMycDB: a database for comparative analysis of mycobacterial genes and genomes Genet Mol Res 5 2006 115 126
18. R.R. Chaudhuri, N.J. Loman, L.A. Snyder, C.M. Bailey, D.J. Stekel, and M.J. Pallen xBASE2: a comprehensive resource for comparative bacterial genomics Nucleic Acids Res 36 2008 D543 D546
19. PathoSystems Resource Integration Center (PATRIC). Available from http://patricbrc.vbi.vt.edu/portal/portal/patric/Taxon?cType=taxon&cId=1763 [accessed 4.04.11].
20. E.J. Alm, K.H. Huang, M.N. Price, R.P. Koche, K. Keller, and I.L. Dubchak The MicrobesOnline Web site for comparative genomics Genome Res 15 2005 1015 1022
21. P.S. Dehal, M.P. Joachimiak, M.N. Price, J.T. Bates, J.K. Baumohl, and D. Chivian MicrobesOnline: an integrated portal for comparative and functional genomics Nucleic Acids Res 38 2010 D396 D400
22. M.N. Price, K.H. Huang, E.J. Alm, and A.P. Arkin A novel method for accurate operon predictions in all sequenced prokaryotes Nucleic Acids Res 33 2005 880 892
23. R.L. Tatusov, E.V. Koonin, and D.J. Lipman A genomic perspective on protein families Science 278 1997 631 637
24. R.L. Tatusov, N.D. Fedorova, J.D. Jackson, A.R. Jacobs, B. Kiryutin, and E.V. Koonin The COG database: an updated version includes eukaryotes BMC Bioinform 4 2003 41
25. World Health Organization: Multidrug and extensively drug-resistant TB (M/XDR-TB): 2010 global report on surveillance and response. Available from http://www.who.int/tb/features-archive/world-tb-day-2010/en/index.html [accessed 4.04.11].
26. A. Sandgren, M. Strong, P. Muthukrishnan, B.K. Weiner, G.M. Church, and M.B. Murray Tuberculosis drug resistance mutation database PLoS Med 6 2009 2
27. Mycobacterium tuberculosis comparative database. Available from http://www.broadinstitute.org/annotation/genome/mycobacterium-tuberculosis-spp/ MultiHome.html [accessed 4.04.11].
28. R. Zhang, and Y. Lin DEG 5.0, a database of essential genes in both prokaryotes and eukaryotes Nucleic Acids Res 37 2009 D455 D458
29. C.M. Sassetti, D.H. Boyd, and E.J. Rubin Genes required for mycobacterial growth defined by high density mutagenesis Mol Microbiol 48 2003 77 84
30. J. Yang, L. Chen, L. Sun, J. Yu, and Q. Jin VFDB 2008 release: an enhanced web-based resource for comparative pathogenomics Nucleic Acids Res 36 2008 D539 D542
31. P.W. Rose, B. Beran, C. Bi, W.F. Bluhm, D. Dimitropoulos, and D.S. Goodsell The RCSB Protein Data Bank: redesigned web site and web services Nucleic Acids Res 39 2011 D392 D401
32. F. Agüero, B. Al-Lazikani, M. Aslett, M. Berriman, F.S. Buckner, and R.K. Campbell Genomic-scale prioritization of drug targets: the TDR Targets database Nat Rev Drug Discov 7 2008 900 907
33. Database of Drug Targets for Resistant Pathogens (DDTRP). Available from http://bmi.icmr.org.in/DDTRP [accessed 4.04.11].
34. H. Ogata, S. Goto, K. Sato, W. Fujibuchi, H. Bono, and M. Kanehisa KEGG: Kyoto encyclopedia of genes and genomes Nucleic Acids Res 27 1999 29 34
35. C.J. Krieger, P. Zhang, L.A. Mueller, A. Wang, S. Paley, and M. Arnaud MetaCyc: a multiorganism database of metabolic pathways and enzymes Nucleic Acids Res 32 2004 D438 D442
36. R. Caspi, T. Altman, J.M. Dale, K. Dreher, C.A. Fulcher, and F. Gilham The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases Nucleic Acids Res 38 2010 D473 D479
37. Y.T. Tang, and G.R. Marshall Virtual screening for lead discovery Methods Mol Biol 716 2011 1 22
38. P. Kolb, R.S. Ferreira, J.J. Irwin, and B.K. Shoichet Docking and chemoinformatic screens for new ligands and targets Curr Opin Biotechnol 20 2009 429 436
39. J.R. Schames, R.H. Henchman, J.S. Siegel, C.A. Sotriffer, H. Ni, and J.A. McCammon Discovery of a novel binding trench in HIV integrase J Med Chem 47 2004 1879 1881
40. G.M. Morris, D.S. Goodsell, R.S. Halliday, R. Huey, and W.E. Hart Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function J Comput Chem 19 1998 1639 1662
41. S.F. Sousa, P.A. Fernandes, and M.J. Ramos Protein-ligand docking: current status and future challenges Proteins 65 2006 15 26
42. K.P. Seiler, G.A. George, M.P. Happ, N.E. Bodycombe, H.A. Carrinski, and S. Norton ChemBank: a small-molecule screening and cheminformatics resource database Nucleic Acids Res 36 2008 D351 D359
43. R.L. Strausberg, and S.L. Schreiber From knowing to controlling: a path from genomics to drugs using small molecule probes Science 300 2003 294 295
44. J.H. Chen, E. Linstead, S.J. Swamidass, D. Wang, and P. Baldi ChemDB update-full-text search and virtual chemical space Bioinformatics 23 2007 2348 2351
45. J.J. Irwin, and B.K. Shoichet ZINC-a free database of commercially available compounds for virtual screening J Chem Inf Model 45 2005 177 182
46. Q. Li, T. Cheng, Y. Wang, and S.H. Bryant PubChem as a public resource for drug discovery Drug Discov Today 15 2010 1052 1057
47. A. Bhardwaj, D. Bhartiya, N. Kumar, and V. Scaria TBrowse: an integrative genomics map of Mycobacterium tuberculosis Tuberculosis (Edinb) 89 2009 386 387