[1] | Soto GE & Hultgren SJ, adhesins. Common themes and variations in architecture and assembly. J Bacteriol. (1999) 181:1059-71. |
[2] | Sauer FG, Pinkner JS, Waksman G & Hultgren SJ. Chaperone priming of pilus subunits facilitates a topological transition that drives fiber formation. Cell. (2002) 111:543-51. |
[3] | Nuccio SP & Baumler AJ. Evolution of the chaperone/usher assembly pathway: fimbrial classification goes Greek. Microbiol Mol Biol Rev. (2007) 71:551-75. |
[4] | Zavialov AV, Berglund J, Pudney AF, Fooks LJ, Ibrahim TM, MacIntyre S et al. Structure and biogenesis of the capsular F1 antigen from Yersinia pestis: preserved folding energy drives fiber formation. Cell. (2003) 113:587-96. |
[5] | Verger D, Bullitt E, Hultgren SJ & Waksman G. Crystal structure of the P pilus rod subunit PapA. PLoS pathogens. (2007) 3:73. |
[6] | Li YF, Poole S, Nishio K, Jang K, Rasulova F, McVeigh A et al. Structure of CFA/I fimbriae from enterotoxigenic Escherichia coli. Proc Natl Acad Sci U S A. (2009) 106:10793-8. |
[7] | Klemm P & Schembri MA. Fimbrial surface display systems in bacteria: from vaccines to random libraries. Microbiology. (2000) 12:3025-32. |
[8] | Dong Z, Zhang Z, Li S, Zhang P & Huang C. CS3 fimbriae of enterotoxigenic Escherichia coli as chimeric expression carriers of heterologous antigenic determinants. Sci China C Life Sci. (1999) 42:128-35. |
[9] | Gao RK, Zhang ZS, Li SQ & Huang CF, Construction of a novel display vector deriving from CS3 fimbriae of human enterotoxigenic Escherichia coli. Yi Chuan Xue Bao. (2001) 28:971-9. |
[10] | Saffar B, Yakhchali B & Arbabi M. Development of a bacterial surface display of hexahistidine peptide using CS3 pili for bioaccumulation of heavy metals. Curr Microbiol. (2007) 55:273-7. |
[11] | Boutet E, Lieberherr D, Tognolli M, Schneider M & Bairoch A. UniProtKB/Swiss-Prot. Methods Mol Biol. (2007) 406:89-112. |
[12] | Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H et al. The Protein Data Bank. Nucleic Acids Res. (2000) 28:235-42. |
[13] | McGinnis S & Madden TL. BLAST: at the core of a powerful and diverse set of sequence analysis tools. Nucleic Acids Res. (2004) 32:W20-25. |
[14] | Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. (1997) 25:3389-402. |
[15] | Eswar N, Eramian D, Webb B, Shen MY & Sali A. Protein structure modeling with Modeller. Methods Mol Biol. (2008) 426:145-59. |
[16] | Shen MY & Sali A. Statistical potential for assessment and prediction of protein structures. Protein Sci. (2006) 15:2507-24. |
[17] | Laskoswki RA, MM, Moss DS & Thorton JM. PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Cryst. (1993) 26:283-91. |
[18] | Wiederstein M & Sippl MJ. Prosa II-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Res. (2007) 35:W407-10. |
[19] | McGuffin LJ & Jones DT. Improvement of the GenTHREADER method for genomic fold recognition. Bioinformatics. (2003) 19:874-81. |
[20] | Shi J, Blundell TL & Mizuguchi K. FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. J Mol Biol. (2001) 310:243-57. |
[21] | Jaroszewski L, Rychlewski L, Li Z, Li W & Godzik A. FFAS03: a server for profile--profile sequence alignments. Nucleic Acids Res. (2005) 33:W284-8. |
[22] | Jones DT. GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences. J Mol Biol. (1999) 287:797-815. |
[23] | Kelley LA & Sternberg MJ. Protein structure prediction on the Web: a case study using the Phyre server. Nat Protoc. (2009) 4:363-71. |
[24] | Arnold K, Bordoli L, Kopp J & Schwede T. The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. Bioinformatics. (2006) 22:195-201. |
[25] | Kiefer F, Arnold K, Kunzli M, Bordoli L & Schwede T. The SWISS-MODEL Repository and associated resources. Nucleic Acids Res. (2009) 37: D387-92. |
[26] | Benkert P, Biasini M & Schwede T. Toward the estimation of the absolute quality of individual protein structure models. Bioinformatics. (2011) 27:343-50. |
[27] | Eisenberg D, Luthy R & Bowie JU. VERIFY3D: assessment of protein models with three-dimensional profiles. Methods Enzymol. (1997) 277:396-404. |
[28] | Geourjon C & Deleage G. SOPM: a self-optimized method for protein secondary structure prediction. Protein Eng. (1994) 7:157-64. |
[29] | Garnier J, Gibrat JF & Robson B. GOR method for predicting protein secondary structure from amino acid sequence. Methods Enzymol. (1996) 266:540-53. |
[30] | Rost B & Sander C. Combining evolutionary information and neural networks to predict protein secondary structure. Proteins. (1994) 19:55-72. |
[31] | Levin JM & Garnier J. Improvements in a secondary structure prediction method based on a search for local sequence homologies and its use as a model building tool. Biochim Biophys Acta. (1988) 955:283-95. |
[32] | Stivala A, Wybrow M, Wirth A, Whisstock JC & Stuckey PJ. Automatic generation of protein structure cartoons with Pro-origami. Bioinformatics. (2011) 27:3315-6. |
[33] | Krissinel E & Henrick K. Inference of macromolecular assemblies from crystalline state. J Mol Biol. (2007) 372:774-97. |
[34] | Baker NA, Sept D, Joseph S, Holst MJ & McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc Natl Acad Sci. (2001) 98:10037-41. |
[35] | DeLano WL. The PyMOL molecular graphics system (2002). http://www.pymol.org. |
[36] | Su Y, Zhou A, Xia X, Li W & Sun Z. Quantitative prediction of protein-protein binding affinity with a potential of mean force considering volume correction. Protein Scie. (2009) 18:2550-8. |
[37] | Sauer FG, Barnhart M, Choudhury D, Knight SD, Waksman G & Hultgren SJ. Chaperone-assisted pilus assembly and bacterial attachment. Curr Opin Struct Biol. (2000) 10:548-56. |
[38] | Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. (1994) 22:4673–80. |
[39] | Brodskii LI, Ivanov VV, Kalaidzidis Ia L, Leontovich AM, Nikolaev VK, Feranchuk SI et al. GeneBee-NET: An Internet based server for biopolymer structure analysis. Biokhimiia. (1995) 60:1221-30. Russian. |
[40] | Doong S H. Protein homology modeling with heuristic search for sequence alignment, In 40th Annual Hawaii International Conference on System Sciences (HICSS’07) 2007, 128-128. |
[41] | Xiang Z, Advances in homology protein structure modeling, Curr Protein Pept Sci, 7 (2006) 217-27. |
[42] | Castrignano T, De Meo PD, Cozzetto D, Talamo IG & Tramontano A. The PMDB Protein Model Database. Nucleic Acids Res. (2006) 34:D306-9. |
[43] | Fiorucci S & Zacharias M. Prediction of protein-protein interaction sites using electrostatic desolvation profiles. Biophys J. (2010) 98:1921-30. |
[44] | Jones S & Thornton JM. Analysis of protein-protein interaction sites using surface patches. J Mol Biol. (1997) 272:121-32. |
[45] | McGuffin LJ, Smith RT, Bryson K, Sorensen SA & Jones DT. High throughput profile-profile based fold recognition for the entire human proteome. BMC bioinformatics. (2006) 7:288. |
[46] | Rayan A. New tips for structure prediction by comparative modeling. Bioinformation. (2009) 3:263-7. |