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Volumn 29, Issue 13, 2013, Pages 1614-1622

Incorporating key position and amino acid residue features to identify general and species-specific Ubiquitin conjugation sites

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; PROTEOME; UBIQUITIN; UBIQUITINATED PROTEIN;

EID: 84879895159     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btt196     Document Type: Conference Paper
Times cited : (113)

References (31)
  • 1
    • 84862641013 scopus 로고    scopus 로고
    • Prediction of lysine ubiquitination with mRMR feature selection and analysis
    • Cai, Y. et al. (2012) Prediction of lysine ubiquitination with mRMR feature selection and analysis. Amino Acids, 42, 1387-1395.
    • (2012) Amino Acids , vol.42 , pp. 1387-1395
    • Cai, Y.1
  • 2
    • 12344310195 scopus 로고    scopus 로고
    • Preferred in vivo ubiquitination sites
    • Catic, A. et al. (2004) Preferred in vivo ubiquitination sites. Bioinformatics, 20, 3302-3307.
    • (2004) Bioinformatics , vol.20 , pp. 3302-3307
    • Catic, A.1
  • 3
    • 58149269554 scopus 로고    scopus 로고
    • Prediction of integral membrane protein type by collocated hydrophobic amino acid pairs
    • Chen, K. et al. (2009) Prediction of integral membrane protein type by collocated hydrophobic amino acid pairs. J. Comput. Chem., 30, 163-172.
    • (2009) J. Comput. Chem. , vol.30 , pp. 163-172
    • Chen, K.1
  • 4
    • 79960909253 scopus 로고    scopus 로고
    • Prediction of Ubiquitination sites by using the composition of k-spaced amino acid pairs
    • Chen, Z. et al. (2011) Prediction of Ubiquitination sites by using the composition of k-spaced amino acid pairs. PLoS One, 6, e22930.
    • (2011) PLoS One , vol.6
    • Chen, Z.1
  • 5
    • 34247559318 scopus 로고    scopus 로고
    • UbiProt: A database of ubiquitylated proteins
    • Chernorudskiy, A.L. et al. (2007) UbiProt: A database of ubiquitylated proteins. BMC Bioinformatics, 8, 126.
    • (2007) BMC Bioinformatics , vol.8 , pp. 126
    • Chernorudskiy, A.L.1
  • 6
    • 2442423854 scopus 로고    scopus 로고
    • Prediction of protein function and pathways in the genome era
    • Gabaldon, T. and Huynen, M.A. (2004) Prediction of protein function and pathways in the genome era. Cell. Mol. Life Sci., 61, 930-944.
    • (2004) Cell. Mol. Life Sci. , vol.61 , pp. 930-944
    • Gabaldon, T.1    Huynen, M.A.2
  • 7
    • 78650153738 scopus 로고    scopus 로고
    • Musite, a tool for global prediction of general and kinasespecific phosphorylation sites
    • Gao, J.J. et al. (2010) Musite, a tool for global prediction of general and kinasespecific phosphorylation sites. Mol. Cell Proteomics, 9, 2586-2600.
    • (2010) Mol. Cell Proteomics , vol.9 , pp. 2586-2600
    • Gao, J.J.1
  • 8
    • 27144529182 scopus 로고    scopus 로고
    • Ubiquitylation and cell signaling
    • Haglund, K. and Dikic, I. (2005) Ubiquitylation and cell signaling. EMBO J., 24, 3353-3359.
    • (2005) EMBO J. , vol.24 , pp. 3353-3359
    • Haglund, K.1    Dikic, I.2
  • 9
    • 0026458378 scopus 로고
    • Amino-acid substitution matrices from protein blocks
    • Henikoff, S. and Henikoff, J.G. (1992) Amino-acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. USA, 89, 10915-10919.
    • (1992) Proc. Natl. Acad. Sci. USA , vol.89 , pp. 10915-10919
    • Henikoff, S.1    Henikoff, J.G.2
  • 10
    • 0242300110 scopus 로고    scopus 로고
    • A subset of membrane-associated proteins is ubiquitinated in response to mutations in the endoplasmic reticulum degradation machinery
    • Hitchcock, A.L. et al. (2003) A subset of membrane-associated proteins is ubiquitinated in response to mutations in the endoplasmic reticulum degradation machinery. Proc. Natl. Acad. Sci. USA, 100, 12735-12740.
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 12735-12740
    • Hitchcock, A.L.1
  • 11
    • 44649101850 scopus 로고    scopus 로고
    • Atypical ubiquitin chains: New molecular signals 'Protein modifications: Beyond the usual suspects review series
    • Ikeda, F and Dikic, I. (2008) Atypical ubiquitin chains: New molecular signals. 'Protein modifications: Beyond the usual suspects' review series. EMBO Rep., 9, 536-542.
    • (2008) EMBO Rep. , vol.9 , pp. 536-542
    • Ikeda, F.1    Dikic, I.2
  • 12
    • 0343621535 scopus 로고    scopus 로고
    • AAindex: Amino acid index database
    • Kawashima, S. and Kanehisa, M. (2000) AAindex: Amino acid index database. Nucleic Acids Res., 28, 374-374.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 374-374
    • Kawashima, S.1    Kanehisa, M.2
  • 13
    • 82455179484 scopus 로고    scopus 로고
    • Systematic and quantitative assessment of the Ubiquitin-modified proteome
    • Kim, W. et al. (2011) Systematic and quantitative assessment of the Ubiquitin-modified proteome. Mol Cell, 44, 325-340.
    • (2011) Mol Cell , vol.44 , pp. 325-340
    • Kim, W.1
  • 14
    • 78149461454 scopus 로고    scopus 로고
    • N-Ace: Using solvent accessibility and physicochemical properties to identify protein N-acetylation sites
    • Lee, T.Y. et al. (2010) N-Ace: Using solvent accessibility and physicochemical properties to identify protein N-acetylation sites. J. Comput. Chem., 31, 2759-2771.
    • (2010) J. Comput. Chem. , vol.31 , pp. 2759-2771
    • Lee, T.Y.1
  • 15
    • 79952369924 scopus 로고    scopus 로고
    • Incorporating distant sequence features and radial basis function networks to identify Ubiquitin conjugation sites
    • Lee, T.Y. et al. (2011) Incorporating distant sequence features and radial basis function networks to identify Ubiquitin conjugation sites. PLoS One, 6, e17331.
    • (2011) PLoS One , vol.6
    • Lee, T.Y.1
  • 16
    • 54049153629 scopus 로고    scopus 로고
    • SCUD: Saccharomyces cerevisiae ubiquitination database
    • Lee, W.C. et al. (2008) SCUD: Saccharomyces cerevisiae Ubiquitination database. BMC Genomics, 9, 440.
    • (2008) BMC Genomics , vol.9 , pp. 440
    • Lee, W.C.1
  • 17
    • 33745634395 scopus 로고    scopus 로고
    • Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences
    • Li, W. and Godzik, A. (2006) Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics, 22, 1658-1659.
    • (2006) Bioinformatics , vol.22 , pp. 1658-1659
    • Li, W.1    Godzik, A.2
  • 18
    • 23044506681 scopus 로고    scopus 로고
    • The ubiquitin-proteasome pathway and its role in cancer
    • Mani, A. and Gelmann, E.P. (2005) The ubiquitin-proteasome pathway and its role in cancer. J. Clin. Oncol., 23, 4776-4789.
    • (2005) J. Clin. Oncol. , vol.23 , pp. 4776-4789
    • Mani, A.1    Gelmann, E.P.2
  • 19
    • 34447527882 scopus 로고    scopus 로고
    • Clustering of phosphorylation site recognition motifs can be exploited to predict the targets of cyclin-dependent kinase
    • Moses, A.M. et al. (2007) Clustering of phosphorylation site recognition motifs can be exploited to predict the targets of cyclin-dependent kinase. Genome Biol., 8, R23.
    • (2007) Genome Biol. , vol.8
    • Moses, A.M.1
  • 20
    • 78649884719 scopus 로고    scopus 로고
    • Prediction of tyrosine sulfation with mRMR feature selection and analysis
    • Niu, S. et al. (2010) Prediction of tyrosine sulfation with mRMR feature selection and analysis. J. Proteome Res., 9, 6490-6497.
    • (2010) J. Proteome Res. , vol.9 , pp. 6490-6497
    • Niu, S.1
  • 21
    • 0041706156 scopus 로고    scopus 로고
    • A proteomics approach to understanding protein ubiquitination
    • Peng, J.M. et al. (2003) A proteomics approach to understanding protein ubiquitination. Nat. Biotechnol., 21, 921-926.
    • (2003) Nat. Biotechnol. , vol.21 , pp. 921-926
    • Peng, J.M.1
  • 22
    • 9744227183 scopus 로고    scopus 로고
    • Ubiquitin: Structures, functions, mechanisms
    • Pickart, C.M. and Eddins, M.J. (2004) Ubiquitin: Structures, functions, mechanisms. BBAMol. Cell Res., 1695, 55-72.
    • (2004) BBAMol. Cell Res. , vol.1695 , pp. 55-72
    • Pickart, C.M.1    Eddins, M.J.2
  • 23
    • 77449103113 scopus 로고    scopus 로고
    • Identification, analysis, and prediction of protein ubiquitination sites
    • Radivojac, P. et al. (2010) Identification, analysis, and prediction of protein ubiquitination sites. Proteins, 78, 365-380.
    • (2010) Proteins , vol.78 , pp. 365-380
    • Radivojac, P.1
  • 24
    • 33750946999 scopus 로고    scopus 로고
    • Narrative review: Protein degradation and human diseases: The ubiquitin connection
    • Reinstein, E. and Ciechanover, A. (2006) Narrative review: Protein degradation and human diseases: The ubiquitin connection. Ann. Intern. Med., 145, 676-684.
    • (2006) Ann. Intern. Med. , vol.145 , pp. 676-684
    • Reinstein, E.1    Ciechanover, A.2
  • 25
    • 78650253267 scopus 로고    scopus 로고
    • Ubiquitylation of an ERAD substrate occurs on multiple types of amino acids
    • Shimizu, Y. et al. (2010) Ubiquitylation of an ERAD substrate occurs on multiple types of amino acids. Mol Cell, 40, 917-926.
    • (2010) Mol Cell , vol.40 , pp. 917-926
    • Shimizu, Y.1
  • 26
    • 34247525565 scopus 로고    scopus 로고
    • Methods for the purification of ubiquitinated proteins
    • Tomlinson, E. et al. (2007) Methods for the purification of ubiquitinated proteins. Proteomics, 7, 1016-1022.
    • (2007) Proteomics , vol.7 , pp. 1016-1022
    • Tomlinson, E.1
  • 27
    • 48249145694 scopus 로고    scopus 로고
    • Computational identification of ubiquitylation sites from protein sequences
    • Tung, C.W. and Ho, S.Y. (2008) Computational identification of ubiquitylation sites from protein sequences. BMC Bioinformatics, 9, 310.
    • (2008) BMC Bioinformatics , vol.9 , pp. 310
    • Tung, C.W.1    Ho, S.Y.2
  • 28
    • 0032594959 scopus 로고    scopus 로고
    • An overview of statistical learning theory
    • Vapnik, V.N. (1999) An overview of statistical learning theory. IEEE. Trans. Neural Netw., 10, 988-999.
    • (1999) IEEE. Trans. Neural Netw. , vol.10 , pp. 988-999
    • Vapnik, V.N.1
  • 29
    • 80054033461 scopus 로고    scopus 로고
    • A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles
    • M111.013284
    • Wagner, S.A. et al. (2011) A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles. Mol. Cell Proteomics, 10, M111.013284.
    • (2011) Mol. Cell Proteomics , vol.10
    • Wagner, S.A.1
  • 30
    • 0346799108 scopus 로고    scopus 로고
    • Prediction of protein function from protein sequence and structure
    • Whisstock, J.C. and Lesk, A.M. (2003) Prediction of protein function from protein sequence and structure. Q. Rev. Biophys., 36, 307-340.
    • (2003) Q. Rev. Biophys. , vol.36 , pp. 307-340
    • Whisstock, J.C.1    Lesk, A.M.2
  • 31
    • 78651225388 scopus 로고    scopus 로고
    • Global analysis of lysine ubiquitination by ubiquitin remnant immunoaffinity profiling
    • Xu, G. et al. (2010) Global analysis of lysine ubiquitination by ubiquitin remnant immunoaffinity profiling. Nat. Biotechnol., 28, 868-873.
    • (2010) Nat. Biotechnol. , vol.28 , pp. 868-873
    • Xu, G.1


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