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The structural motif discovery method presented herein is general and can be …

Biology Articles » Biochemistry » Protein Biochemistry » Discovering structural motifs using a structural alphabet: Application to magnesium-binding sites » References

- Discovering structural motifs using a structural alphabet: Application to magnesium-binding sites

  1. Cowan JA: Biological Chemistry of Magnesium.New York , VCH; 1995.

  2. Nordlund P, Sjoberg BM, Eklund H: Three-dimensional structure of the free radical protein of ribonucleotide reductase.

    Nature 1990, 345:593.

  3. Dudev T, Cowan JA, Lim C: Competitive Binding in Magnesium Coordination Chemistry: Water versus Ligands of Biological Interest.

    J Am Chem Soc 1999, 121:7665-7673.

  4. Cowan JA: Metal activation of enzymes in nucleic acid biochemistry.

    Chem Rev 1998, 98:1067-1087.

  5. Chotia C, Lesk AM: The relation between the divergence of sequence and structure in proteins.

    EMBO J 1986, 5:823-826.

  6. de Brevern AG, Etchebest C, Hazout S: Bayesian probabilistic approach for predicting backbone structures in terms of protein blocks.

    Proteins: Struct Funct Genet 2000, 41:271-287.

  7. de Brevern AG: New assessment of a structural alphabet.

    In Silico Biol 2005, 5:26.

  8. Unger R, Sussman JL: The importance of short structural motifs in protein structure analysis.

    J Comput Aided Mol Des 1993, 7:457-472.

  9. Tyagi M, Sharma P, Swamy CS, Cadet F, Srinivasan N, de Brevern AG, Offman B: Protein block expert (PBE): a web-based protein structure analysis server using a structural alphabet.

    Nucleic Acids Res 2006, 34:W119-W123.

  10. Tyagi M, Gowri VS, Srinivasan N, de Brevern AG, Offmann B: A substitution matrix for structural alphabet based on structural alignment of homologous proteins and its applications.

    Proteins: Structure, Function & Bioinformatics 2006 , 65(1):32-39.

  11. Bystroff C, Baker D: Prediction of local structure in proteins using a library of sequence- structure motifs.

    J Mol Biol 1998, 281(3):565-577.

  12. Kolodny R, Koehl P, Guibas L, Levitt M: Small libraries of protein fragments model native structures accurately.

    J Mol Biol 2002, 323:297-307.

  13. Fourrier L, Benros C, de Brevern AG: Use of a structural alphabet for analysis of short loops connecvting repetitive structures.

    BMC Bioinformatics 2004, 5:58.

  14. Dudev T, Lin YL, Dudev M, Lim C: First-Second Shell Interactions in Metal Binding Sites in Proteins: A PDB Survey and DFT/CDM Calculations.

    J Am Chem Soc 2003, 125:3168-3180.

  15. Petkovich M, Brand NJ, Krust A, Chambon P: A human retinoic acid receptor which belongs to the family of nuclear receptors.

    Nature 1987, 330:444-450.

  16. Berman HM, Battistuz T, Bhat TN, Bluhm WF, Bourne PE, Burkhardt K, Iype L, Jain S, Fagan P, Marvin J, Padilla D, Ravichandran V, Schneider B, Thanki N, Weissig H, Westbrook JD, Zardecki C: The Protein Data Bank.

    Acta Crystallogr D 2002, 58:899-907.

  17. Sigrist CJ, Cerutti L, Hulo N, Gattiker A, Falquet L, Pagni M, Bairoch A, Bucher P: PROSITE: a documented database using patters and profiles as motif desriptors.

    Brief Bioinform 2002, 3:265-274.

  18. Dudev T, Lim C: Principles Governing Mg, Ca, and Zn Binding and Selectivity in Proteins.

    Chem Rev 2003, 103:773-787.

  19. Lahiri SD, Zhang GF, Dunaway-Mariano D, Allen KN: Diversification of function in the haloacid dehalogenase enzyme superfamily: The role of the cap domain in hydrolytic phosphorussingle bondcarbon bond cleavage.

    Bioinorg Chem 2006, 34:394-409.

  20. Iding H, Dunnwald T, Greiner L, Liese A, Muller M, Siegert P, Grotzinger J, Demir AS, Pohl M: Benzoylformate decarboxylase from Pseudomonas putida as stable catalyst for the synthesis of chiral 2-hydroxy ketones.

    Chemistry -A Eur J 2000, 6:1483-1495.

  21. Watson JD, Laskowski RA, Thornton JM: Predicting protein function from sequence and structural data.

    Curr Op Struct Biol 2005, 15:275-284.

  22. Kristensen DM, Chen BY, Fofanov VY, Ward RM, Lisewski AM, Kimmel M, Kavraki L, Lichtarge O: Recurrent use of evolutionary importance for functional annotation of proteins based on local structural similarity.

    Prot Sci 2006, 15:1530-1536.

  23. Mathura VS, Schein CH, Braun W: Identifying property based sequence motifs in protein families and superfamilies: application to DNase-1 related endonucleases.

    Proteins: Structure, Function and Bioinformatics 2003, 19:1381-1390.

  24. Schein CH, Zhou B, Oezguen N, Mathura VS, Braun W: Molego-based definition of the architecture and specificity of metal-binding sites.

    Proteins: Structure, Function and Bioinformatics 2005, 58:200-210.

  25. Laskowski RA: PDBsum: summaries and analyses of PDB structures.

    Nucleic Acids Res 2001, 29(1):221-222.

  26. Allen FH: The Cambridge structural database: a quarter of a million crystal structures and rising.

    Acta Cryst 2002, B58:380-388.

  27. Harding MM: The geometry of metal-ligand interactions relevant to proteins.

    Acta Cryst 1999, D55:1432-1443.

  28. McDonald IK, Thornton JM: Satisfying hydrogen bonding potential in proteins.

    J Mol Biol 1994, 238(5):777-793.

  29. Jonassen I, Eidhammer I, Conklin D, Taylor WR: Structure motif discovery and mining the PDB.

    Bioinformatics 2001, 18:362-367.

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