DBMODELING: A database applied to the study of protein targets from genome projects

Cell Biochemistry and Biophysics

Volumn 44, Issue 3, 2006, Pages 366-374

  Da Silveira, Nelson José Freitas ^a   Bonalumi, Carlos Eduardo ^a   Uchôa, Hugo Brandão ^a   Pereira, José Henrique ^a   Canduri, Fernanda ^b   De Azevedo Jr , Walter Filgueira ^c  

^a SÃO PAULO STATE UNIVERSITY UNESP   (Brazil)

^b FEDERAL UNIVERSITY OF MATO GROSSO DO SUL   (Brazil)

^c PONTIFICAL CATHOLIC UNIVERSITY OF RIO GRANDE DO SUL   (Brazil)

Author keywords

Bioinformatics; Database; Drug design; Homology modeling; Metabolic pathway; Protein structure

Indexed keywords

PROTEIN;

ANIMAL; BACTERIAL GENOME; CHEMICAL STRUCTURE; CHEMISTRY; CONFERENCE PAPER; DATA BASE; DRUG DESIGN; FACTUAL DATABASE; GENETIC DATABASE; GENETICS; GENOME; HUMAN; INFORMATION RETRIEVAL; INSTRUMENTATION; INTERNET; METHODOLOGY; MYCOBACTERIUM TUBERCULOSIS; PROTEIN DATABASE; SEQUENCE HOMOLOGY; STATISTICS; STRUCTURAL HOMOLOGY; THREE DIMENSIONAL IMAGING; XYLELLA;

ANIMALS; DATABASE MANAGEMENT SYSTEMS; DATABASES, FACTUAL; DATABASES, GENETIC; DATABASES, PROTEIN; DRUG DESIGN; GENOME; GENOME, BACTERIAL; HUMANS; IMAGING, THREE-DIMENSIONAL; INFORMATION STORAGE AND RETRIEVAL; INTERNET; MODELS, MOLECULAR; MYCOBACTERIUM TUBERCULOSIS; PROTEINS; SEQUENCE HOMOLOGY, AMINO ACID; SEQUENCE HOMOLOGY, NUCLEIC ACID; STRUCTURAL HOMOLOGY, PROTEIN; XYLELLA;

MYCOBACTERIUM TUBERCULOSIS; XYLELLA FASTIDIOSA;

EID: 33646887220     PISSN: 10859195     EISSN: None     Source Type: Journal    
DOI: 10.1385/CBB:44:3:366     Document Type: Conference Paper

References (49)

1. da Silveira, N. J. F., Uchôa, H. B., Pereira, J. H., et al. (2005) Molecular models of protein targets from Mycobacterium tuberculosis. J. Mol. Model. 11, 160-166.
2. Word Health Organization (2001) Global tuberculosis control. WHO Report 2001. Geneva, Switzerland, WHO/ CDS/TB/2001, 287.
3. Simpson, A. J., Reinach, F. C., Arruda, P., et al. (2002) The genome sequence of the plant pathogen Xylella fastidiosa. Nature 406, 151-157.
4. Bevan, M. (2002) The bugs from Brazil. Nature 406, 140-141.
5. Ealick, S. E., Babu, Y. S., Bugg, C. E., et al. (1991) Application of crystllographic and modeling methods in the design of purine nucleoside phosphorylase inhibitors. Proc. Natl. Acad. Sci. U.S.A. 88, 11,540-11,544.
6. Veerapandian, P. (1997) Structure-Based Drug Design (Veerapandian, P., ed.), Marcel Dekker, New York.
7. de Azevedo, W. F., Jr., Mueller-Dieckmann, H. J., Schulze-Gahmen, U., Worland, P. J., Sausville, E., and Kim, S. H. (1996) Structural basis for specificity and potency of a flavonoid inhibitor of human CDK2, a cell cycle kinase. Proc. Natl. Acad. Sci. U.S.A.. 93, 2735-2740.
8. de Azevedo, W. F., Jr., Leclerc, S., Meijer, L., Havlicek, L., Strnad, M., and Kim, S. H. (1997) Inhibition of cyclin-dependent kinases by purine analogues: crystal structure of human cdk2 complexed with roscovitine. Eur. J. Biochem. 243, 518-526.
9. Foster, M. J. (2002) Molecular modeling in structural biology. Micron 33, 365-384.
10. Ring, C. S., Sun, E., McKerrow, J. G., Lee, G. K., Rosenthal, P. J., Kuntz, I. D., and Cohen, F. E. (1993) Structure-based inhibitor design by using protein models for the development of antiparasitic agents. Proc. Natl. Acad. Sci. U.S.A. 90, 3583-3587.
11. Selzer, P. M., Chen, X., Chan, V. J., et al. (1997) Leishmania major: molecular modeling of cysteine proteases and prediction of new nonpeptide inhibitors. Exp. Parasitol. 87, 212-221.
12. Que, X., Brinen, L. S., Perkins, P., et al. (2002) Cysteine proteinases from distinct cellular compartments are recruited to phagocytic vesicles by Entamoeba histolytica. Mol. Biochem. Parasitol. 119, 23-32.
13. Sali, A. and Blundell, T. L. (1993) Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234, 779-815.
14. Blundell, T. L., Jhoti, H., and Abell, C. (2002) High-throughput crystallography for lead discovery in drug design. Nat. Rev. 1, 45-54.
15. Jacobson, M. and Sali, A. (2004) Comparative protein structure modeling and its applications to drug discovery. Annu. Rep. Med. Chem. 39, 259-276.
16. Anderson, A. C. (2003) The process of structure-based drug design. Chem. Biol. 10, 787-797.
17. Karp, P. D. (2001) Pathway databases: a case study in computational symbolic theories. Science 293, 2040-2044.
18. Edgar, R. C. and Kimmen, S. (2004) COACH: profile-profile alignment of roteins families using hidden Markov models. Bioinformatics 20, 1309-1308.
19. 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.
20. Kanehisa, M. (2000) Post-genome Informatics, Oxford University Press, New York.
21. Browne, W. J., North, A. C., Phillips, D. C., Drew, K., Vanaman, T. C. and Hill, R. L. (1969) A possible three-dimensional structure of bovine alpha-lactalbumin based on that of hen's egg-white lysozyme. J. Mol. Biol. 42, 65-86.
22. Sánchez, R. and Sali, A. (1999) ModBase: a database of comparative protein structure models. Bioinformatics 15, 1060-1061.
23. Gerstein, M. and Levitt, M. (1997) Structural census of the current population of protein sequences. Proc. Natl. Acad. Sci. U.S.A. 94, 11,911-11,916.
24. Fischer, D. and Eisenberg, D. (1999) Predicting structures for genome proteins. Curr. Opin. Struct. Biol. 9, 208-211.
25. Uchoa, H. B., Jorge, G. E., da Silveira, N. J. F., Câmera, J. C., Jr., Canduri, F., and de Azevedo, W. F., Jr. (2004) Parmodel: a Web server for automated comparative modeling of proteins. Biochem. Biophys. Res. Commun. 325, 1481-1486.
26. MacKerell, A.D.J., Bashford, D., Bellott, R. L., et al. (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B 102, 3586-3616.
27. Laskowski, R. A., MacArthur, M. W., and Thornton, J. M. (1998) Validation of proteins derived from experiment. Curr. Opin. Struct. Biol. 8, 631-639.
28. Wilson, C., Gregoret, L. M., and Agard, D. A. (1993) Modeling side-chain conformation for homologous proteins using an energy-based rotamers search. J. Mol. Biol. 229, 996-1006.
29. Laskowski, R. A., MacArthurm, M. W., Smith, D. K., et al. (1994) PROCHECK v.3.0 - program to check the stereo-chemistry quality of protein structures - operating instructions.
30. Hooft, R. W., Sander, C., and Vriend, G. (1996) Positioning hydrogen atoms by optimizing hydrogen-bond networks in proteins structures. Proteins 26, 363-376.
31. Bowie, J. U., Luthy R., and Eisenberg, D. (1991) A method to identify protein sequences that fold into a known three-dimensional structure. Science 253, 164-170.
32. Kabsch, W. and Sander, C. (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22, 2577-2637.
33. Sippl, M. J. (1990) Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins. J. Mol. Biol. 213, 859-883.
34. Luthy, R., Bowie, J. U. and Eisenberg, K. (1992) Assessment of protein models with three-dimensional profiles. Nature 356, 83-85.
35. Arcuri, H. A., Canduri, F., Pereira, J. H., et al. (2004) Molecular models for shikimate pathway enzymes of Xylella fastidiosa. Biochem. Biophys. Res. Commun. 320, 979-991.
36. da Silveira, N.J.F., Uchoa, H. B., Canduri, F., et al. (2004) Structural bioinformatics study of PNP from Schistosoma mansoni. Biochem. Biophys. Res. Commun. 322, 100-104.
37. Brünger, A.T. (1992) X-PLOR, A System for Crystallography and NMR, Version 3.1, Yale University Press, New Haven, CT.
38. EU 3-D Validation Network (1998) Who checks the checkers? Four validation tools applied to eight atomic resolution structures. J. Mol. Biol. 276, 417-436.
39. DuBois, P. (2000) MySQL, New Riders, Indianapolis, IN.
40. Pieper, U., Eswar, N., Braberg, H., et al. (2004) MODBASE, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res. 32, D217-D222.
41. Kawabata, T., Fukuchi, S., Homma, K., et al. (2002) GTOP: a database of protein structures predicted from genome sequences. Nucleic Acids Res. 30, 294-298.
42. Ogata, H., Goto, S., Sato, K., Fujibuchi, W., Bono, H., and Kanehisa, M. (1999) KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 27, 29-34.
43. Karp, P. D., Riley M., Paley S. M. and Pellegrini-Toole, A. (2002) The MetaCyc Database. Nucleic Acids Res. 30, 59-61.
44. Coggins, J. R., Abell, C., Evans, L. B., et al. (2003) Experiences with the shikimate-pathway enzymes as targets for rational drug design. Biochem. Soc. Trans. 31, 548-552.
45. Campbell, S. A., Richards, T. A., Mui, E. J., et al. (2004) A complete shikimate pathway in Toxoplasma gondii: an ancient eukaryotic innovation. Int. J. Parasitol. 34, 5-13.
46. Herman, K. M. and Weaver, L. M. (1999) The shikimate pathway. Annu. Rev. Plant Mol. Biol. 50, 473-503.
47. de Azevedo, W. F., Jr., Canduri, F., de Oliveira, J. S., et al. (2002) Molecular model of shikimate kinase from Mycobacterium tuberculosis. Biochem. Biophys. Res. Commun. 295, 142-148.
48. Pereira, J. H., Canduri, F., de Oliveira, J. S., et al. (2003) Structural bioinformatics study of EPSP synthase from Mycobacterium tuberculosis. Biochem. Biophys. Res. Commun. 312, 608-614.
49. Pereira, J. H., Oliveira, J. S., Canduri, F., et al. (2004) Structure of shikimate kinase from Mycobacterium tuberculosis reveals the binding of shikimic acid. Acta Crystallogr. D. Biol. Crystallogr. 60, 2310-2319.