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Protein-Carbohydrate interactions are crucial in many biological processes with implications to drug …

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- Sequence and structural features of carbohydrate binding in proteins and assessment of predictability using a neural network

  1. Shionyu-Mitsuyama C, Shirai T, Ishida H, Yamane T: An empirical approach for structure-based prediction of carbohydrate binding sites on proteins.

    Protein Eng 2003, 16:467-78.

  2. Scripps []

  3. Scripps []

  4. Sharon N, Lis H: Lectins as cell recognition molecules.

    Science 1989, 246:227-234.

  5. Lasky LA: Selectins: interpreters of cell-specific carbohydrate information during inflammation.

    Science 1992, 258:964-969.

  6. Sastry K, Ezekowitz RA: Collectins: pattern recognition molecules involved in first line host defense.

    Curr Opin Immunol 1993, 5:59-66.

  7. Barondes SH, Cooper DN, Gitt MA, Leffler H: Galectins: Structure and function of a large family of animal lectins.

    J Biol Chem 1994, 269:20807-10.

  8. Hoppe HJ, Reid KB: Collectins – soluble proteins containing collagenous regions and lectin domains – and their roles in innate immunity.

    Protein Sci 1994, 3:1143-58.

  9. Rosen SD, Bertozzi CR: The selectins and their ligands.

    Curr Opin Cell Biol 1994, 6:663-73.

  10. Sharon N, Lis H: Lectins-proteins with a sweet tooth: function in cell recognition.

    Essays Biochem 1995, 30:59-75.

  11. Sharon NH, Lis H: Lectins: Carbohydrate-Specific Proteins That Mediate Cellular Recognition.

    Chem Rev 1998, 98:637-674.

  12. Karlsson KA: Meaning and therapeutic potential of microbial recognition of host glycoconjugates.

    Mol Microbio 1998, 29:1-11.

  13. Audette GF, Delbaere LT, Xiang J: Mapping protein: carbohydrate interactions.

    Curr Protein Pept Sci 2003, 4:11-20.

  14. Quiocho FA: Protein-carbohydrate interactions: basic molecular features.

    Pure & Appl Chem 1989, 61:1293-1306.

  15. Vyas NK: Atomic features of protein-carbohydrate interactions.

    Curr Opin Struct Biol 1991, 1:732-740.

  16. Spurlino JC, Rodseth LE, Quiocho FA: Atomic interactions in protein-carbohydrate complexes. Tryptophan residues in the periplasmic maltodextrin receptor for active transport and chemotaxis.

    J Mol Biol 1992, 226:15-22.

  17. Toone EJ: Structure and energetics of protein-carbohydrate complexes.

    Curr Opin Struct Biol 1994, 4:719-728.

  18. Meyer JE, Schulz GE: Energy profile of maltooligosaccharide permeation through maltoporin as derived from the structure and from a statistical analysis of saccharide-protein interactions.

    Protein Sci 1997, 6:1084-91.

  19. Rini JM: Lectin structure.

    Annu Rev Biophys Biomol Struct 1995, 24:51-77.

  20. Weis WI, Drickamer K: Structural basis of lectin-carbohydrate recognition.

    Annu Rev Biochem 1996, 65:441-73.

  21. Elgavish S, Shaanan B: Lectin-carbohydrate interactions: different folds, common recognition principles.

    Trends Biochem Sci 1997, 22:462-7.

  22. Rao VS, Lam K, Qasba PK: Architecture of the sugar binding sites in carbohydrate binding proteins – a computer modeling study.

    Int J Biol Macromol 1998, 23:295-307.

  23. Garcia-Hernandez E, Hernandez-Arana A: Structural bases of lectin-carbohydrate affinities: comparison with protein-folding energetics.

    Protein Sci 1999, 8:1075-86.

  24. Garcia-Hernandez E, Zubillaga RA, Rodriguez-Romero A, Hernandez-Arana A: Stereochemical metrics of lectin-carbohydrate interactions: comparison with protein-protein interfaces.

    Glycobiology 2000, 10:993-1000.

  25. Clarke C, Woods RJ, Gluska J, Cooper A, Nutley MA, Boons GJ: Involvement of water in carbohydrate-protein binding.

    J Am Chem Soc 2001, 123:12238-47.

  26. Neumann D, Kohlbacher O, Lenhof HP, Lehr CM: Lectin-sugar interaction. Calculated versus experimental binding energies.

    Eur J Biochem 2002, 269:1518-24

  27. Taroni C, Jones S, Thornton JM (2): Analysis and prediction of carbohydrate binding sites.

    Protein Eng 2000, 13:89-98.

  28. Ahmad S, Gromiha MM, Sarai A: Analysis and prediction of DNA-binding proteins and their binding residues based on composition, sequence and structural information.

    Bioinformatics 2004, 20:477-86.

  29. Ahmad S, Sarai A: PSSM-based prediction of DNA binding sites in proteins.

    BMC Bioinformatics 2005, 6:33.

  30. Wang L, Brown SJ: BindN: a web-based tool for efficient prediction of DNA and RNA binding sites in amino acid sequences.

    Nucleic Acids Res 2006, 34:W243-248.

  31. Kuznetsov IB, Gou Z, Li R, Hwang S: Using evolutionary and structural information to predict DNA-binding sites on DNA-binding proteins.

    Proteins 2006, 64:19-27.

  32. Yan C, Terribilini M, Wu F, Jernigan RL, Dobbs D, Honavar V: Predicting DNA-binding sites of proteins from amino acid sequence.

    BMC Bioinformatics 2006, 7:262.

  33. Fariselli P, Pazos F, Valencia A, Casadio R: Prediction of protein-protein interaction sites in heterocomplexes with neural networks.

    Eur J Biochem 2002, 269:1356-1361.

  34. Jones S, Thornton JM: Prediction of protein-protein interaction sites using patch analysis.

    J Mol Biol 1997, 272:133-143.

  35. Lu L, Lu H, Skolnick J: MULTIPROSPECTOR: an algorithm for the prediction of protein-protein interactions by multimeric threading.

    Proteins 2002, 49:350-64.

  36. Keskin O, Ma B, Rogale K, Gunasekaran K, Nussinov R: Protein-protein interactions: organization, cooperativity and mapping in a bottom-up Systems Biology approach.

    Phys Biol 2005, 2:S24-S35.

  37. Raih MF, Ahmad S, Zheng R, Mohamed R: Solvent accessibility in native and isolated domain environments: general features and implications to interface predictability.

    Biophys Chem 2005, 114:63-9.

  38. Hoskins J, Lovell S, Blundell TL: An algorithm for predicting protein-protein interaction sites: Abnormally exposed amino acid residues and secondary structure elements.

    Protein Sci 2006, 15:1017-29.

  39. Julenius K, Molgaard A, Gupta R, Brunak S: Prediction, conservation analysis, and structural characterization of mammalian mucin-type O-glycosylation sites.

    Glycobiology 2005, 15:153-64.

  40. Blom N, Gammeltoft S, Brunak S: Sequence and structure-based prediction of eukaryotic protein phosphorylation sites.

    J Mol Biol 1999, 94:1351-62.

  41. Spiwok V, Lipovova P, Skalova T, Vondrackova E, Dohnalek J, Hasek J, Kralova B: Modelling of carbohydrate-aromatic interactions: ab initio energetics and force field performance.

    J Comput Aided Mol Des 2005, 19:887-901.

  42. McLean BW, Bray MR, Boraston AB, Gilkes NR, Haynes CA, Kilburn DG: Analysis of binding of the family 2a carbohydrate-binding module from Cellulomonas fimi xylanase 10A to cellulose: specificity and identification of functionally important amino acid residues.

    Protein Eng 2000, 13:801-9.

  43. Poole DM, Hazlewood GP, Huskisson NS, Virden R, Gilbert HJ: The role of conserved tryptophan residues in the interaction of a bacterial cellulose-binding domain with its ligand.

    FEMS Microbiol Lett 1993, 106:77-83.

  44. Din N, Forsythe IJ, Burtnick LD, Gilkes NR, Miller RC Jr, Warren RA, Kilburn DG: The cellulose-binding domain of endoglucanase A (CenA) from Cellulomonas fimi: evidence for the involvement of tryptophan residues in binding.

    Mol Microbiol 1994, 11:747-55.

  45. Bray MR, Johnson PE, Gilkes NR, McIntosh LP, Kilburn DG, Warren RA: Probing the role of tryptophan residues in a cellulose-binding domain by chemical modification.

    Protein Sci 1996, 5:2311-8.

  46. Reinikainen T, Ruohonen L, Nevanen T, Laaksonen L, Kraulis P, Jones TA, Knowles JK, Teeri TT: Investigation of the function of mutated cellulose-binding domains of Trichoderma reesei cellobiohydrolase I.

    Proteins 1992, 14:475-82.

  47. Nagy T, Simpson P, Williamson MP, Hazlewood GP, Gilbert HJ, Orosz L: All three surface tryptophans in Type IIa cellulose binding domains play a pivotal role in binding both soluble and insoluble ligands.

    FEBS Lett 1998, 429:312-6.

  48. Simpson HD, Barras F: Functional analysis of the carbohydrate-binding domains of Erwinia chrysanthemi Cel5 (Endoglucanase Z) and an Escherichia coli putative chitinase.

    J Bacteriol 1999, 18:4611-6.

  49. Ponyi T, Szabo L, Nagy T, Orosz L, Simpson PJ, Williamson MP, Gilbert HJ: Trp22, Trp24, and Tyr8 play a pivotal role in the binding of the family 10 cellulose-binding module from Pseudomonas xylanase A to insoluble ligands.

    Biochemistry 2000, 39:985-91.

  50. Raghothama S, Simpson PJ, Szabo L, Nagy T, Gilbert HJ, Williamson MP: Solution structure of the CBM10 cellulose binding module from Pseudomonas xylanase A.

    Biochemistry 2000, 39:978-84.

  51. CBM []

  52. Gao S, An J, Wu CF, Gu Y, Chen F, Yu Y, Wu QQ, Bao JK: Effect of amino acid residue and oligosaccharide chain chemical modifications on spectral and hemagglutinating activity of Millettia dielsiana Harms. ex Diels. lectin.

    Acta Biochim Biophys Sin (Shanghai) 2005, 37:47-54.

  53. Wang J, Stuckey JA, Wishart MJ, Dixon JE: A unique carbohydrate-binding domain targets the lafora disease phosphatase to glycogen.

    J Biol Chem 2002, 277:2377-80.

  54. Dahms NM, Rose PA, Molkentin JD, Zhang Y, Brzycki MA: The bovine mannose 6-phosphate/insulin-like growth factor II receptor. The role of arginine residues in mannose 6-phosphate binding.

    J Biol Chem 1993, 268:5457-63.

  55. Arauzo-Bravo M, Ahmad S, Sarai A: " Dimensionality of amino acid space and solvent accessibility prediction with neural networks".

    Comput Bio Chem 2006, 30:160-168.

  56. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool.

    J Mol Biol 1990, 215:403-410.

  57. Sujatha MS, Balaji PV: Identification of common structural features of binding sites in galactose-specific proteins.

    Proteins 2004, 5:44-65.

  58. Puvanendrampillai D, Mitchell JB: L/D Protein Ligand Database (PLD): additional understanding of the nature and specificity of protein-ligand complexes.

    Bioinformatics 2003, 19:1856-7.

  59. Li W, Jaroszewski L, Godzik A: Clustering of highly homologous sequences to reduce the size of large protein database.

    Bioinformatics 2001, 17:282-283.

  60. Apweiler R, Bairoch A, Wu CH: Protein sequence databases.

    Curr Opin in Chem Biol 2004, 8:76-80.

  61. Bairoch A, Boeckmann B: The SWISS-PROT protein sequence data bank.

    Nucleic Acids Res 1991, 19:2247-2249.

  62. NCBI BLAST database download site []

  63. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

    Nucleic Acids Res 1997, 25:3389-3402.

  64. Ahmad S, Gromiha M, Fawareh H, Sarai A: ASAView: database and tool for solvent accessibility representation in proteins.

    BMC Bioinformatics 2004, 5:51.

  65. Kabsch W, Sander C: Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features.

    Biopolymers 1983, 22:2577-637.

  66. SNNS []

  67. Ahmad S, Gromiha MM: Design and training of a neural network for predicting the solvent accessibility of proteins.

    J Comput Chem 2003, 24:1313-1320.

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