MtbSD-A comprehensive structural database for Mycobacterium tuberculosis

Tuberculosis

Volumn 91, Issue 6, 2011, Pages 556-562

  Hassan, Sameer ^a   Logambiga, P ^a   Raman, A Mohan ^a   Subazini, T K ^b   Kumaraswami, V ^a   Hanna, Luke Elizabeth ^a  

^a NATIONAL INSTITUTE FOR RESEARCH IN TUBERCULOSIS   (India)

^b ANNA UNIVERSITY   (India)

Author keywords

Database; Domains; Ligands; Mycobacterium tuberculosis; Proteins

Indexed keywords

BACTERIAL PROTEIN; INHA PROTEIN; ISONIAZID; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; BACTERIAL GENOME; DATA BASE; MOLECULAR DOCKING; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN STRUCTURE; SCREENING; SEQUENCE ALIGNMENT;

BACTERIAL PROTEINS; DATABASE MANAGEMENT SYSTEMS; DATABASES, PROTEIN; DRUG DESIGN; HUMANS; INFORMATION STORAGE AND RETRIEVAL; INTERNET; MOLECULAR SEQUENCE DATA; MYCOBACTERIUM TUBERCULOSIS; SEQUENCE ANALYSIS, PROTEIN; USER-COMPUTER INTERFACE;

EID: 80755163485     PISSN: 14729792     EISSN: 1873281X     Source Type: Journal    
DOI: 10.1016/j.tube.2011.08.003     Document Type: Article

References (22)

1. World Health Organisation Global tuberculosis control: a short update to the 2009 report 2009
2. Directorate of Health Services, Ministry of Health and family welfare, www.tbcindia.org.2009.
3. S.T. Cole, R. Brosch, J. Parkhill, T. Garnier, C. Churcher, D. Harris, S.V. Gordon, K. Eiglmeier, S. Gas, C.E. Barry 3rd, F. Tekaia, K. Badcock, D. Basham, D. Brown, T. Chillingworth, R. Connor, R. Davies, K. Devlin, T. Feltwell, S. Gentles, N. Hamlin, S. Holroyd, T. Hornsby, K. Jagels, A. Krogh, J. McLean, S. Moule, L. Murphy, K. Oliver, J. Osborne, M.A. Quail, M.A. Rajandream, J. Rogers, S. Rutter, K. Seeger, J. Skelton, R. Squares, S. Squares, J.E. Sulston, K. Taylor, S. Whitehead, and B.G. Barrell Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence Nature 393 1998 537 544 (Pubitemid 28319235)
4. T.I. Zarembinski, L.W. Hung, H.J. Mueller-Dieckmann, K.K. Kim, H. Yokota, R. Kim, and S.H. Kim Structure-based assignment of the biochemical function of a hypothetical protein: a test case of structural genomics Proc Natl Acad Sci U S A 95 1998 15189 15193 (Pubitemid 29018674)
5. S.H. Kim Shining a light on structural genomics Nat Struct Biol 5 Suppl. 1998 643 645
6. R. Koike, T. Amemiya, M. Ota, and A. Kidera Protein structural change upon ligand binding correlates with enzymatic reaction mechanism J Mol Biol 379 2008 397 401
7. S.L. McGovern, and B.K. Shoichet Information decay in molecular docking screens against holo, apo, and modeled conformations of enzymes J Med Chem 46 2003 2895 2907 (Pubitemid 36775915)
8. G.L. Warren, C.W. Andrews, A.M. Capelli, B. Clarke, J. LaLonde, M.H. Lambert, M. Lindvall, N. Nevins, S.F. Semus, S. Senger, G. Tedesco, I.D. Wall, J.M. Woolven, C.E. Peishoff, and M.S. Head A critical assessment of docking programs and scoring functions J Med Chem 49 2006 5912 5931 (Pubitemid 44484938)
9. C.W. Murray, C.A. Baxter, and A.D. Frenkel The sensitivity of the results of molecular docking to induced fit effects: application to thrombin, thermolysin and neuraminidase J Comput Aided Mol Des 13 1999 547 562 (Pubitemid 29524912)
10. B. Boeckmann, A. Bairoch, R. Apweiler, M.C. Blatter, A. Estreicher, E. Gasteiger, M.J. Martin, K. Michoud, C. O'Donovan, I. Phan, S. Pilbout, and M. Schneider The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003 Nucleic Acids Res 31 2003 365 370 (Pubitemid 36157284)
11. M. Bashton, I. Nobeli, and J.M. Thornton PROCOGNATE: a cognate ligand domain mapping for enzymes Nucleic Acids Res 36 2008 D618 D622
12. T.L. Musa, T.R. Ioerger, and J.C. Sacchettini The tuberculosis structural genomics consortium: a structural genomics approach to drug discovery Adv Protein Chem Struct Biol 77 2009 41 76
13. A. Kapopoulou, J.M. Lew, and S.T. Cole The MycoBrowser portal: a comprehensive and manually annotated resource for mycobacterial genomes Tuberculosis (Edinb) 91 2011 8 13
14. J.E. Galagan, P. Sisk, C. Stolte, B. Weiner, M. Koehrsen, F. Wymore, T.B. Reddy, J.D. Zucker, R. Engels, M. Gellesch, J. Hubble, H. Jin, L. Larson, M. Mao, M. Nitzberg, J. White, Z.K. Zachariah, G. Sherlock, C.A. Ball, and G.K. Schoolnik TB database 2010: overview and update Tuberculosis (Edinb) 90 2010 225 235
15. J.L. Sussman, D. Lin, J. Jiang, N.O. Manning, J. Prilusky, O. Ritter, and E.E. Abola Protein Data Bank (PDB): database of three-dimensional structural information of biological macromolecules Acta Crystallogr D Biol Crystallogr 54 1998 1078 1084 (Pubitemid 29000162)
16. M. Johnson, I. Zaretskaya, Y. Raytselis, Y. Merezhuk, S. McGinnis, and T.L. Madden NCBI BLAST: a better web interface Nucleic Acids Res 36 2008 W5 W9
17. F. Aguero, B. Al-Lazikani, M. Aslett, M. Berriman, F.S. Buckner, R.K. Campbell, S. Carmona, I.M. Carruthers, A.W. Chan, F. Chen, G.J. Crowther, M.A. Doyle, C. Hertz-Fowler, A.L. Hopkins, G. McAllister, S. Nwaka, J.P. Overington, A. Pain, G.V. Paolini, U. Pieper, S.A. Ralph, A. Riechers, D.S. Roos, A. Sali, D. Shanmugam, T. Suzuki, W.C. Van Voorhis, and C.L. Verlinde Genomic-scale prioritization of drug targets: the TDR targets database Nat Rev Drug Discov 7 2008 900 907
18. R.L. Tatusov, N.D. Fedorova, J.D. Jackson, A.R. Jacobs, B. Kiryutin, E.V. Koonin, D.M. Krylov, R. Mazumder, S.L. Mekhedov, A.N. Nikolskaya, B.S. Rao, S. Smirnov, A.V. Sverdlov, S. Vasudevan, Y.I. Wolf, J.J. Yin, and D.A. Natale The COG database: an updated version includes eukaryotes BMC Bioinform 4 2003 41
19. S.A. Rahman, M. Bashton, G.L. Holliday, R. Schrader, and J.M. Thornton Small Molecule Subgraph Detector (SMSD) toolkit J Cheminform 1 2009 12
20. M. Kanehisa, and S. Goto KEGG: kyoto encyclopedia of genes and genomes Nucleic Acids Res 28 2000 27 30 (Pubitemid 30047706)
21. R.D. Finn, J. Mistry, J. Tate, P. Coggill, A. Heger, J.E. Pollington, O.L. Gavin, P. Gunasekaran, G. Ceric, K. Forslund, L. Holm, E.L. Sonnhammer, S.R. Eddy, and A. Bateman The Pfam protein families database Nucleic Acids Res 38 2010 D211 D222
22. L. Lo Conte, S.E. Brenner, T.J. Hubbard, C. Chothia, and A.G. Murzin SCOP database in 2002: refinements accommodate structural genomics Nucleic Acids Res 30 2002 264 267 (Pubitemid 34679560)