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Volumn 415, Issue 1, 2012, Pages 193-204

Prediction of short linear protein binding regions

Author keywords

intrinsically unstructured proteins; linear motif; molecular recognition; peptide binding; protein protein interface

Indexed keywords

ACCURACY; AMINO ACID SEQUENCE; ARTICLE; BINDING SITE; BIOCHEMISTRY; BIOPHYSICS; MACHINE LEARNING; PREDICTIVE VALIDITY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN FUNCTION; PROTEIN MOTIF; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; SHORT LINEAR MOTIF PREDICTOR; SHORT LINEAR PROTEIN BINDING REGION;

EID: 84855278383     PISSN: 00222836     EISSN: 10898638     Source Type: Journal    
DOI: 10.1016/j.jmb.2011.10.025     Document Type: Article
Times cited : (65)

References (46)
  • 1
    • 14644435825 scopus 로고    scopus 로고
    • Intrinsically unstructured proteins and their functions
    • DOI 10.1038/nrm1589
    • Dyson, H. & Wright, P. (2005). Intrinsically unstructured proteins and their functions. Nat. Rev. Mol. Cell Biol. 6, 197-208. (Pubitemid 40314921)
    • (2005) Nature Reviews Molecular Cell Biology , vol.6 , Issue.3 , pp. 197-208
    • Dyson, H.J.1    Wright, P.E.2
  • 2
    • 34249695447 scopus 로고    scopus 로고
    • Local structural disorder imparts plasticity on linear motifs
    • Fuxreiter, M., Tompa, P. & Simon, I. (2007). Local structural disorder imparts plasticity on linear motifs. Bioinformatics, 23, 950.
    • (2007) Bioinformatics , vol.23 , pp. 950
    • Fuxreiter, M.1    Tompa, P.2    Simon, I.3
  • 3
    • 77956636245 scopus 로고    scopus 로고
    • Computational identification and analysis of protein short linear motifs
    • Davey, N., Edwards, R. & Shields, D. (2010). Computational identification and analysis of protein short linear motifs. Front. Biosci. 15, 801-825.
    • (2010) Front. Biosci. , vol.15 , pp. 801-825
    • Davey, N.1    Edwards, R.2    Shields, D.3
  • 6
    • 79952154955 scopus 로고    scopus 로고
    • Characterization of a novel JNK (c-Jun N-terminal kinase) inhibitory peptide
    • Ngoei, K., Catimel, B., Church, N., Lio, D., Dogovski, C., Perugini, M. et al. (2011). Characterization of a novel JNK (c-Jun N-terminal kinase) inhibitory peptide. Biochem. J. 434, 399-413.
    • (2011) Biochem. J. , vol.434 , pp. 399-413
    • Ngoei, K.1    Catimel, B.2    Church, N.3    Lio, D.4    Dogovski, C.5    Perugini, M.6
  • 7
    • 78651277460 scopus 로고    scopus 로고
    • PHOSIDA 2011: The posttranslational modification database
    • Database Issue
    • Gnad, F., Gunawardena, J. & Mann, M. (2010). PHOSIDA 2011: the posttranslational modification database. Nucleic Acids Res. 39, D253-D260; (Database Issue).
    • (2010) Nucleic Acids Res. , vol.39
    • Gnad, F.1    Gunawardena, J.2    Mann, M.3
  • 10
    • 33747824163 scopus 로고    scopus 로고
    • DILIMOT: Discovery of linear motifs in proteins
    • Web Server Issue
    • Neduva, V. & Russell, R. B. (2006). DILIMOT: discovery of linear motifs in proteins. Nucleic Acids Res. 34, W350-W355; (Web Server Issue).
    • (2006) Nucleic Acids Res. , vol.34
    • Neduva, V.1    Russell, R.B.2
  • 11
    • 23144445962 scopus 로고    scopus 로고
    • QuasiMotiFinder: Protein annotation by searching for evolutionarily conserved motif-like patterns
    • DOI 10.1093/nar/gki496
    • Gutman, R., Berezin, C., Wollman, R., Rosenberg, Y. &Ben-Tal, N. (2005). QuasiMotiFinder: protein annotation by searching for evolutionarily conserved motiflike patterns. Nucleic Acids Res. 33, W255-W261. (Pubitemid 44529920)
    • (2005) Nucleic Acids Research , vol.33 , Issue.WEB. SERV. ISS.
    • Gutman, R.1    Berezin, C.2    Wollman, R.3    Rosenberg, Y.4    Ben-Tal, N.5
  • 12
    • 75849140545 scopus 로고    scopus 로고
    • Evidence for the concerted evolution between short linear protein motifs and their flanking regions
    • Chica, C., Diella, F. & Gibson, T. J. (2009). Evidence for the concerted evolution between short linear protein motifs and their flanking regions. PLoS ONE, 4, e6052.
    • (2009) PLoS ONE , vol.4
    • Chica, C.1    Diella, F.2    Gibson, T.J.3
  • 13
    • 60149099647 scopus 로고    scopus 로고
    • Masking residues using context-specific evolutionary conservation significantly improves short linear motif discovery
    • Davey, N. E., Shields, D. C. & Edwards, R. J. (2009). Masking residues using context-specific evolutionary conservation significantly improves short linear motif discovery. Bioinformatics, 25, 443-450.
    • (2009) Bioinformatics , vol.25 , pp. 443-450
    • Davey, N.E.1    Shields, D.C.2    Edwards, R.J.3
  • 14
    • 52249101769 scopus 로고    scopus 로고
    • Short linear motifs recognized by SH2, SH3 and Ser/Thr kinase domains are conserved in disordered protein regions
    • Ren, S., Uversky, V. N., Chen, Z., Dunker, K. K. &Obradovic, Z. (2008). Short linear motifs recognized by SH2, SH3 and Ser/Thr kinase domains are conserved in disordered protein regions. BMC Genomics, 9, S26.
    • (2008) BMC Genomics , vol.9
    • Ren, S.1    Uversky, V.N.2    Chen, Z.3    Dunker, K.K.4    Obradovic, Z.5
  • 16
    • 41149162675 scopus 로고    scopus 로고
    • NestedMICA as an ab initio protein motif discovery tool
    • Dogruel, M., Down, T. A. & Hubbard, T. J. (2008). NestedMICA as an ab initio protein motif discovery tool. BMC Bioinf. 9, 19.
    • (2008) BMC Bioinf. , vol.9 , pp. 19
    • Dogruel, M.1    Down, T.A.2    Hubbard, T.J.3
  • 17
    • 79959984707 scopus 로고    scopus 로고
    • SLiMSearch 2.0 biological context for short linear motifs in proteins
    • Web Server Issue
    • Davey, N. E., Haslam, N. J., Shields, D. C. & Edwards, R. J. (2011). SLiMSearch 2.0 biological context for short linear motifs in proteins. Nucleic Acids Res. 39, W56-W60; (Web Server Issue).
    • (2011) Nucleic Acids Res. , vol.39
    • Davey, N.E.1    Haslam, N.J.2    Shields, D.C.3    Edwards, R.J.4
  • 18
  • 19
    • 77949732319 scopus 로고    scopus 로고
    • From proteome lists to biological impact - Tools and strategies for the analysis of large MS data sets
    • Malik, R., Dulla, K., Nigg, E. A. & Koerner, R. (2010). From proteome lists to biological impact - tools and strategies for the analysis of large MS data sets. Proteomics, 10, 1270-1283.
    • (2010) Proteomics , vol.10 , pp. 1270-1283
    • Malik, R.1    Dulla, K.2    Nigg, E.A.3    Koerner, R.4
  • 21
    • 24044538903 scopus 로고    scopus 로고
    • IUPred: Web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content
    • DOI 10.1093/bioinformatics/bti541
    • Dosztányi, Z., Csizmok, V., Tompa, P. & Simon, I. (2005). IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content. Bioinformatics, 21, 3433-3434. (Pubitemid 41222453)
    • (2005) Bioinformatics , vol.21 , Issue.16 , pp. 3433-3434
    • Dosztanyi, Z.1    Csizmok, V.2    Tompa, P.3    Simon, I.4
  • 23
    • 3242891318 scopus 로고    scopus 로고
    • The DISOPRED server for the prediction of protein disorder
    • DOI 10.1093/bioinformatics/bth195
    • Ward, J. J., McGuffin, L. J., Bryson, K., Buxton, B. F. &Jones, D. T. (2004). The DISOPRED server for the prediction of protein disorder. Bioinformatics, 20, 2138-2139. (Pubitemid 39236567)
    • (2004) Bioinformatics , vol.20 , Issue.13 , pp. 2138-2139
    • Ward, J.J.1    McGuffin, L.J.2    Bryson, K.3    Buxton, B.F.4    Jones, D.T.5
  • 24
    • 58149163609 scopus 로고    scopus 로고
    • KEPE - A motif frequently superimposed on SUMOylation sites in metazoan chromatin proteins and transcription factors
    • Diella, F., Chabanis, S., Luck, K., Chica, C., Ramu, C., Nerlov, C. & Gibson, T. J. (2009). KEPE - a motif frequently superimposed on SUMOylation sites in metazoan chromatin proteins and transcription factors. Bioinformatics, 25, 1-5.
    • (2009) Bioinformatics , vol.25 , pp. 1-5
    • Diella, F.1    Chabanis, S.2    Luck, K.3    Chica, C.4    Ramu, C.5    Nerlov, C.6    Gibson, T.J.7
  • 26
    • 67049119327 scopus 로고    scopus 로고
    • Prediction of protein binding regions in disordered proteins
    • Mészáros, B., Simon, I. & Dosztányi, Z. (2009). Prediction of protein binding regions in disordered proteins. PLoS Comput. Biol. 5, e1000376.
    • (2009) PLoS Comput. Biol. , vol.5
    • Mészáros, B.1    Simon, I.2    Dosztányi, Z.3
  • 29
    • 67049119327 scopus 로고    scopus 로고
    • Prediction of protein binding regions in disordered proteins
    • Meszaros, B., Simon, I. & Dosztanyi, Z. (2009). Prediction of protein binding regions in disordered proteins. PLoS Comput. Biol. 5, e1000376.
    • (2009) PLoS Comput. Biol. , vol.5
    • Meszaros, B.1    Simon, I.2    Dosztanyi, Z.3
  • 30
    • 70349996473 scopus 로고    scopus 로고
    • ANCHOR: Web server for predicting protein binding regions in disordered proteins
    • Dosztányi, Z., Mészáros, B. & Simon, I. (2009). ANCHOR: web server for predicting protein binding regions in disordered proteins. Bioinformatics, 25, 2745-2746.
    • (2009) Bioinformatics , vol.25 , pp. 2745-2746
    • Dosztányi, Z.1    Mészáros, B.2    Simon, I.3
  • 31
    • 24944546549 scopus 로고    scopus 로고
    • Coupled folding and binding with alpha-helix-forming molecular recognition elements
    • DOI 10.1021/bi050736e
    • Oldfield, C., Cheng, Y., Cortese, M., Romero, P., Uversky, V. & Dunker, A. (2005). Coupled folding and binding with α-helix-forming molecular recognition elements. Biochemistry, 44, 12454-12470. (Pubitemid 41324337)
    • (2005) Biochemistry , vol.44 , Issue.37 , pp. 12454-12470
    • Oldfield, C.J.1    Cheng, Y.2    Cortese, M.S.3    Romero, P.4    Uversky, V.N.5    Dunker, A.K.6
  • 32
    • 36749037699 scopus 로고    scopus 로고
    • Mining alpha-helix-forming molecular recognition features with cross species sequence alignments
    • DOI 10.1021/bi7012273
    • Cheng, Y., Oldfield, C., Meng, J., Romero, P., Uversky, V. & Dunker, A. (2007). Mining α-helix-forming molecular recognition features with cross species sequence alignments. Biochemistry, 46, 13468-13477. (Pubitemid 350209945)
    • (2007) Biochemistry , vol.46 , Issue.47 , pp. 13468-13477
    • Cheng, Y.1    Oldfield, C.J.2    Meng, J.3    Romero, P.4    Uversky, V.N.5    Dunker, A.K.6
  • 34
    • 40949117264 scopus 로고    scopus 로고
    • Flexible nets: Disorder and induced fit in the associations of p53 and 14-3-3 with their partners
    • Oldfield, C., Meng, J., Yang, J., Yang, M., Uversky, V. & Dunker, A. (2008). Flexible nets: disorder and induced fit in the associations of p53 and 14-3-3 with their partners. BMC Genomics, 9, S1.
    • (2008) BMC Genomics , vol.9
    • Oldfield, C.1    Meng, J.2    Yang, J.3    Yang, M.4    Uversky, V.5    Dunker, A.6
  • 35
    • 0034663990 scopus 로고    scopus 로고
    • The structure and function of the beta2-adaptin appendage domain
    • Owen, D., Vallis, Y., Pearse, B., McMahon, H. &Evans, P. (2000). The structure and function of the β2-adaptin appendage domain. EMBO J. 19, 4216-4227. (Pubitemid 30623732)
    • (2000) EMBO Journal , vol.19 , Issue.16 , pp. 4216-4227
    • Owen, D.J.1    Vallis, Y.2    Pearse, B.M.F.3    McMahon, H.T.4    Evans, P.R.5
  • 36
    • 17444397116 scopus 로고    scopus 로고
    • Porter: A new, accurate server for protein secondary structure prediction
    • DOI 10.1093/bioinformatics/bti203
    • Pollastri, G. & McLysaght, A. (2005). Porter: a new, accurate server for protein secondary structure prediction. Bioinformatics, 21, 1719-1720. (Pubitemid 40542742)
    • (2005) Bioinformatics , vol.21 , Issue.8 , pp. 1719-1720
    • Pollastri, G.1    McLysaght, A.2
  • 37
    • 75849153303 scopus 로고    scopus 로고
    • The Universal Protein Resource (UniProt) in 2010
    • UniProt Consortium. Database Issue
    • UniProt Consortium. (2010). The Universal Protein Resource (UniProt) in 2010. Nucleic Acids Res. 38, D142-D148; (Database Issue).
    • (2010) Nucleic Acids Res. , vol.38
  • 38
    • 43349092663 scopus 로고    scopus 로고
    • CompariMotif: Quick and easy comparisons of sequence motifs
    • DOI 10.1093/bioinformatics/btn105
    • Edwards, R. J., Davey, N. E. & Shields, D. C. (2008). CompariMotif: quick and easy comparisons of sequence motifs. Bioinformatics, 24, 1307-1309. (Pubitemid 351659630)
    • (2008) Bioinformatics , vol.24 , Issue.10 , pp. 1307-1309
    • Edwards, R.J.1    Davey, N.E.2    Shields, D.C.3
  • 39
    • 58149194624 scopus 로고    scopus 로고
    • SMART 6: Recent updates and new developments
    • Database Issue
    • Letunic, I., Doerks, T. & Bork, P. (2009). SMART 6: recent updates and new developments. Nucleic Acids Res. 37, D229-D232; (Database Issue).
    • (2009) Nucleic Acids Res. , vol.37
    • Letunic, I.1    Doerks, T.2    Bork, P.3
  • 40
    • 34547127137 scopus 로고    scopus 로고
    • Accurate prediction of protein secondary structure and solvent accessibility by consensus combiners of sequence and structure information
    • Pollastri, G., Martin, A. J. M., Mooney, C. & Vullo, A. (2007). Accurate prediction of protein secondary structure and solvent accessibility by consensus combiners of sequence and structure information. BMC Bioinf. 8, 201.
    • (2007) BMC Bioinf. , vol.8 , pp. 201
    • Pollastri, G.1    Martin, A.J.M.2    Mooney, C.3    Vullo, A.4
  • 41
    • 39049179145 scopus 로고    scopus 로고
    • Protein structural motif prediction in multidimensional ø-ψ space leads to improved secondary structure prediction
    • Mooney, C., Vullo, A. & Pollastri, G. (2006). Protein structural motif prediction in multidimensional ø-ψ space leads to improved secondary structure prediction. J. Comput. Biol. 13, 1489-1502.
    • (2006) J. Comput. Biol. , vol.13 , pp. 1489-1502
    • Mooney, C.1    Vullo, A.2    Pollastri, G.3
  • 42
    • 77955476975 scopus 로고    scopus 로고
    • Novel peptide-mediated interactions derived from high-resolution 3-dimensional structures
    • Stein, A. & Aloy, P. (2010). Novel peptide-mediated interactions derived from high-resolution 3-dimensional structures. PLoS Comput. Biol. 6, e1000789.
    • (2010) PLoS Comput. Biol. , vol.6
    • Stein, A.1    Aloy, P.2
  • 44
    • 0033369033 scopus 로고    scopus 로고
    • Exploiting the past and the future in protein secondary structure prediction
    • Baldi, P., Brunak, S., Frasconi, P., Soda, G. & Pollastri, G. (1999). Exploiting the past and the future in protein secondary structure prediction. Bioinformatics, 15, 937.
    • (1999) Bioinformatics , vol.15 , pp. 937
    • Baldi, P.1    Brunak, S.2    Frasconi, P.3    Soda, G.4    Pollastri, G.5
  • 45
    • 33749139123 scopus 로고    scopus 로고
    • Distill: A suite of web servers for the prediction of one-, two- and three-dimensional structural features of proteins
    • Baú, D., Martin, A. J. M., Mooney, C., Vullo, A., Walsh, I. & Pollastri, G. (2006). Distill: a suite of web servers for the prediction of one-, two- and three-dimensional structural features of proteins. BMC Bioinf. 7, 402.
    • (2006) BMC Bioinf. , vol.7 , pp. 402
    • Baú, D.1    Martin, A.J.M.2    Mooney, C.3    Vullo, A.4    Walsh, I.5    Pollastri, G.6
  • 46
    • 14844342815 scopus 로고    scopus 로고
    • The pairwise energy content estimated from amino acid composition discriminates between folded and intrinsically unstructured proteins
    • DOI 10.1016/j.jmb.2005.01.071
    • Dosztányi, Z., Csizmók, V., Tompa, P. & Simon, I. (2005). The pairwise energy content estimated from amino acid composition discriminates between folded and intrinsically unstructured proteins. J. Mol. Biol. 347, 827-839. (Pubitemid 40357923)
    • (2005) Journal of Molecular Biology , vol.347 , Issue.4 , pp. 827-839
    • Dosztanyi, Z.1    Csizmok, V.2    Tompa, P.3    Simon, I.4


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