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Volumn 8, Issue 6, 2013, Pages

In silico Platform for Prediction of N-, O- and C-Glycosites in Eukaryotic Protein Sequences

Author keywords

[No Author keywords available]

Indexed keywords

GLYCOPROTEIN;

EID: 84879546356     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0067008     Document Type: Article
Times cited : (199)

References (33)
  • 1
  • 3
    • 33845528552 scopus 로고    scopus 로고
    • Clinical applications of glycomic approaches for the detection of cancer and other diseases
    • Miyamoto S, (2006) Clinical applications of glycomic approaches for the detection of cancer and other diseases. Curr Opin Mol Ther 8: 507-513.
    • (2006) Curr Opin Mol Ther , vol.8 , pp. 507-513
    • Miyamoto, S.1
  • 4
    • 3943059566 scopus 로고    scopus 로고
    • Roles of N-linked glycans in the endoplasmic reticulum
    • Helenius A, Aebi M, (2004) Roles of N-linked glycans in the endoplasmic reticulum. Annu Rev Biochem 73: 1019-1049.
    • (2004) Annu Rev Biochem , vol.73 , pp. 1019-1049
    • Helenius, A.1    Aebi, M.2
  • 5
    • 0035937505 scopus 로고    scopus 로고
    • Intracellular Functions of N-linked glycans
    • Helenius A, Aebi M, (2001) Intracellular Functions of N-linked glycans. Science 291: 2364-2369.
    • (2001) Science , vol.291 , pp. 2364-2369
    • Helenius, A.1    Aebi, M.2
  • 6
    • 0025367812 scopus 로고
    • Sequence differences between glycosylated and non-glycosylated Asn-X-Thr/Ser acceptor sites: implications for protein engineering
    • Gavel Y, von Heijne G, (1990) Sequence differences between glycosylated and non-glycosylated Asn-X-Thr/Ser acceptor sites: implications for protein engineering. Protein Eng 3(5): 433-442.
    • (1990) Protein Eng , vol.3 , Issue.5 , pp. 433-442
    • Gavel, Y.1    von Heijne, G.2
  • 7
    • 0017871099 scopus 로고
    • Glycosyl transfer from dolichyl phosphate sugars to endogenous and exogenous glycoprotein acceptors in yeast
    • Lehle L, Tanner W, (1978) Glycosyl transfer from dolichyl phosphate sugars to endogenous and exogenous glycoprotein acceptors in yeast. Eur J Biochem 83(2): 563-570.
    • (1978) Eur J Biochem , vol.83 , Issue.2 , pp. 563-570
    • Lehle, L.1    Tanner, W.2
  • 8
    • 0025865091 scopus 로고
    • Amino acid distributions around O-linked glycosylation sites
    • Wilson B, Gavel Y, von Heijne G, (1991) Amino acid distributions around O-linked glycosylation sites. Biochem J 275: 529-534.
    • (1991) Biochem J , vol.275 , pp. 529-534
    • Wilson, B.1    Gavel, Y.2    von Heijne, G.3
  • 9
    • 0035146448 scopus 로고    scopus 로고
    • Database analysis of O-glycosylation sites in proteins
    • Christlet THT, Veluraja K, (2001) Database analysis of O-glycosylation sites in proteins. Biophys J 80: 952-960.
    • (2001) Biophys J , vol.80 , pp. 952-960
    • Christlet, T.H.T.1    Veluraja, K.2
  • 10
    • 0031882332 scopus 로고    scopus 로고
    • Recognition Signal for C-Mannosylation of Trp-7 in RNase 2 Consists of Sequence Trp-x-x-Trp
    • Krieg J, Hartmann S, Vicentini A, Glasner W, Hess D, et al. (1998) Recognition Signal for C-Mannosylation of Trp-7 in RNase 2 Consists of Sequence Trp-x-x-Trp. Mol Biol Cell 9: 301-309.
    • (1998) Mol Biol Cell , vol.9 , pp. 301-309
    • Krieg, J.1    Hartmann, S.2    Vicentini, A.3    Glasner, W.4    Hess, D.5
  • 11
  • 12
    • 84863611053 scopus 로고    scopus 로고
    • GlycoPP: A Webserver for Prediction of N- and O-Glycosites in Prokaryotic Protein Sequences
    • Chauhan JS, Bhat AH, Raghava GP, Rao A, (2012) GlycoPP: A Webserver for Prediction of N- and O-Glycosites in Prokaryotic Protein Sequences. PLoS One 7(7): e40155.
    • (2012) PLoS One , vol.7 , Issue.7
    • Chauhan, J.S.1    Bhat, A.H.2    Raghava, G.P.3    Rao, A.4
  • 13
    • 80052479968 scopus 로고    scopus 로고
    • Similarities and differences in the glycosylation mechanisms in prokaryotes and eukaryotes
    • Dell A, Galadari A, Sastre F, Hitchen P (2010) Similarities and differences in the glycosylation mechanisms in prokaryotes and eukaryotes. Int J Microbiol: 148-178.
    • (2010) Int J Microbiol , pp. 148-178
    • Dell, A.1    Galadari, A.2    Sastre, F.3    Hitchen, P.4
  • 14
    • 77955713515 scopus 로고    scopus 로고
    • N-Linked glycoengineering for human therapeutic proteins in bacteria
    • Pandhal J, Wright PC, (2010) N-Linked glycoengineering for human therapeutic proteins in bacteria. Biotechnol Lett. 32(9): 1189-98.
    • (2010) Biotechnol Lett , vol.32 , Issue.9 , pp. 1189-1198
    • Pandhal, J.1    Wright, P.C.2
  • 16
    • 0033600935 scopus 로고    scopus 로고
    • Prediction of Potential GPI-modification Sites in Protein Sequences
    • Eisenhaber B, Bork P, Eisenhaber F, (1999) Prediction of Potential GPI-modification Sites in Protein Sequences. J Mol Biol 292: 741-758.
    • (1999) J Mol Biol , vol.292 , pp. 741-758
    • Eisenhaber, B.1    Bork, P.2    Eisenhaber, F.3
  • 17
    • 0031809552 scopus 로고    scopus 로고
    • NetOglyc: prediction of mucin type O-glycosylation sites based on sequence context and surface accessibility
    • Hansen JE, Lund O, Tolstrup N, Gooley AA, Williams KL, et al. (1998) NetOglyc: prediction of mucin type O-glycosylation sites based on sequence context and surface accessibility. Glycoconj J 15: 115-130.
    • (1998) Glycoconj J , vol.15 , pp. 115-130
    • Hansen, J.E.1    Lund, O.2    Tolstrup, N.3    Gooley, A.A.4    Williams, K.L.5
  • 18
    • 13644257223 scopus 로고    scopus 로고
    • Prediction, conservation analysis and structural characterization of mammalian mucin-type O-glycosylation sites
    • Julenius K, Mølgaard A, Gupta R, Brunak S, (2005) Prediction, conservation analysis and structural characterization of mammalian mucin-type O-glycosylation sites. Glycobiology 15: 153-164.
    • (2005) Glycobiology , vol.15 , pp. 153-164
    • Julenius, K.1    Mølgaard, A.2    Gupta, R.3    Brunak, S.4
  • 19
    • 33646887253 scopus 로고    scopus 로고
    • Predicting O-glycosylation sites in mammalian proteins by using SVMs
    • Li S, Liu B, Zeng R, Cai Y, Li Y, (2006) Predicting O-glycosylation sites in mammalian proteins by using SVMs. Comput Biol Chem 30(3): 203-208.
    • (2006) Comput Biol Chem , vol.30 , Issue.3 , pp. 203-208
    • Li, S.1    Liu, B.2    Zeng, R.3    Cai, Y.4    Li, Y.5
  • 20
    • 0036370537 scopus 로고    scopus 로고
    • Prediction of glycosylation across the human proteome and the correlation to protein function
    • Gupta R, Brunk S, (2002) Prediction of glycosylation across the human proteome and the correlation to protein function. Pacific Symposium on Biocpmputing 7: 310-322.
    • (2002) Pacific Symposium on Biocpmputing , vol.7 , pp. 310-322
    • Gupta, R.1    Brunk, S.2
  • 21
    • 2942564430 scopus 로고    scopus 로고
    • Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence
    • Blom N, Sicheritz-Ponten T, Gupta R, Gammeltoft S, Brunak S, (2004) Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence. Proteomics 4(6): 1633-1649.
    • (2004) Proteomics , vol.4 , Issue.6 , pp. 1633-1649
    • Blom, N.1    Sicheritz-Ponten, T.2    Gupta, R.3    Gammeltoft, S.4    Brunak, S.5
  • 22
    • 38849163717 scopus 로고    scopus 로고
    • Glycosylation site prediction using ensembles of Support Vector Machine classifiers
    • Caragea C, Sinapov J, Silvescu A, Dobbs D, Honavar V, (2007) Glycosylation site prediction using ensembles of Support Vector Machine classifiers. BMC Bioinformatics 8: 438.
    • (2007) BMC Bioinformatics , vol.8 , pp. 438
    • Caragea, C.1    Sinapov, J.2    Silvescu, A.3    Dobbs, D.4    Honavar, V.5
  • 23
    • 62149135362 scopus 로고    scopus 로고
    • Prediction of glycosylation sites using random forests
    • Hamby SE, Hirst JD, (2008) Prediction of glycosylation sites using random forests. BMC Bioinformatics 9: 500.
    • (2008) BMC Bioinformatics , vol.9 , pp. 500
    • Hamby, S.E.1    Hirst, J.D.2
  • 24
    • 61649126270 scopus 로고    scopus 로고
    • Predicting protein post-translational modifications using meta-analysis of proteome scale data sets
    • Schwartz D, Chou MF, Church GM, (2009) Predicting protein post-translational modifications using meta-analysis of proteome scale data sets. Mol Cell Proteomics. 8(2): 365-79.
    • (2009) Mol Cell Proteomics , vol.8 , Issue.2 , pp. 365-379
    • Schwartz, D.1    Chou, M.F.2    Church, G.M.3
  • 25
    • 76749092270 scopus 로고    scopus 로고
    • The WEKA Data Mining Sogftware: An Update SIGKDD Explorations
    • Hall M, Frank E, Holmes G, Pfahringer B, Reutemann P, (2009) The WEKA Data Mining Sogftware: An Update SIGKDD Explorations. 11(1): 10-18.
    • (2009) , vol.11 , Issue.1 , pp. 10-18
    • Hall, M.1    Frank, E.2    Holmes, G.3    Pfahringer, B.4    Reutemann, P.5
  • 27
    • 0002714543 scopus 로고    scopus 로고
    • Making large scale SVM learning practical
    • Scholkopf B, Burges C, Smola A, editors, Cambridge: MIT Press
    • Joachims T (1999) Making large scale SVM learning practical. Scholkopf B, Burges C, Smola A, editors. Advances in kernel methods: Support Vector Learning. Cambridge: MIT Press 169-184.
    • (1999) Advances in kernel methods: Support Vector Learning , pp. 169-184
    • Joachims, T.1
  • 28
    • 40549105098 scopus 로고    scopus 로고
    • Prediction of RNA binding sites in a protein using SVM and PSSM profile
    • Kumar M, Gromiha M, Raghava GPS, (2007) Prediction of RNA binding sites in a protein using SVM and PSSM profile. Proteins 71: 189-194.
    • (2007) Proteins , vol.71 , pp. 189-194
    • Kumar, M.1    Gromiha, M.2    Raghava, G.P.S.3
  • 29
    • 77952971734 scopus 로고    scopus 로고
    • Prediction of GTP interacting residues, dipeptides and tripeptides in a protein from its evolutionary information
    • Chauhan JS, Mishra NK, Raghava GPS, (2010) Prediction of GTP interacting residues, dipeptides and tripeptides in a protein from its evolutionary information. BMC Bioinformatics 11: 301.
    • (2010) BMC Bioinformatics , vol.11 , pp. 301
    • Chauhan, J.S.1    Mishra, N.K.2    Raghava, G.P.S.3
  • 30
    • 0034044314 scopus 로고    scopus 로고
    • The PSIPRED protein structure prediction server
    • McGuffin LJ, Bryson K, Jones DT, (2000) The PSIPRED protein structure prediction server. Bioinformatics 16(4): 404-5.
    • (2000) Bioinformatics , vol.16 , Issue.4 , pp. 404-405
    • McGuffin, L.J.1    Bryson, K.2    Jones, D.T.3
  • 31
    • 26444473604 scopus 로고    scopus 로고
    • Real value prediction of solvent accessibility in proteins using multiple sequence alignment and secondary structure
    • Garg A, Kaur H, Raghava GPS, (2005) Real value prediction of solvent accessibility in proteins using multiple sequence alignment and secondary structure. Proteins 61(2): 318-324.
    • (2005) Proteins , vol.61 , Issue.2 , pp. 318-324
    • Garg, A.1    Kaur, H.2    Raghava, G.P.S.3
  • 32
    • 84867623385 scopus 로고    scopus 로고
    • Prediction of lysine post-translational modifications using bioinformatic tools
    • Schwartz D, (2012) Prediction of lysine post-translational modifications using bioinformatic tools. Essays Biochem 52: 165-77.
    • (2012) Essays Biochem , vol.52 , pp. 165-177
    • Schwartz, D.1
  • 33
    • 0032919585 scopus 로고    scopus 로고
    • O-GLYCBASE version 4.0: a revised database of O-glycosylated proteins
    • Gupta R, Birch H, Rapacki K, Brunak S, Hansen J, (1999) O-GLYCBASE version 4.0: a revised database of O-glycosylated proteins. Nucleic Acids Res 27: 370-372.
    • (1999) Nucleic Acids Res , vol.27 , pp. 370-372
    • Gupta, R.1    Birch, H.2    Rapacki, K.3    Brunak, S.4    Hansen, J.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.