메뉴 건너뛰기




Volumn 28, Issue 12, 2012, Pages

MoRFpred, a computational tool for sequence-based prediction and characterization of short disorder-to-order transitioning binding regions in proteins

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; PROTEIN;

EID: 84863518014     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts209     Document Type: Article
Times cited : (305)

References (46)
  • 1
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
    • Altschul, S. et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
    • (1997) Nucleic Acids Res , vol.25 , pp. 3389-3402
    • Altschul, S.1
  • 2
    • 10844225367 scopus 로고    scopus 로고
    • Principal eigenvector of contact matrices and hydrophobicity profiles in proteins
    • Bastolla, U. et al. (2005) Principal eigenvector of contact matrices and hydrophobicity profiles in proteins. Proteins, 58, 22-30.
    • (2005) Proteins , vol.58 , pp. 22-30
    • Bastolla, U.1
  • 3
    • 33846036096 scopus 로고    scopus 로고
    • The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data
    • Berman, H. et al. (2007) The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Res., 35, D301-D303.
    • (2007) Nucleic Acids Res , vol.35
    • Berman, H.1
  • 4
    • 3242802943 scopus 로고    scopus 로고
    • Studies of the RNA degradosome-organizing domain of the Escherichia coli ribonucleaseRNase E
    • Callaghan, A.J. et al. (2004) Studies of the RNA degradosome-organizing domain of the Escherichia coli ribonucleaseRNase E. J. Mol. Biol., 340, 965-979.
    • (2004) J. Mol. Biol. , vol.340 , pp. 965-979
    • Callaghan, A.J.1
  • 5
    • 33645778262 scopus 로고    scopus 로고
    • Conservation of intrinsic disorder in protein domains and families: I. Adatabase of conserved predicted disordered regions
    • Chen, J.W. et al. (2006a) Conservation of intrinsic disorder in protein domains and families: I. Adatabase of conserved predicted disordered regions. J. Proteome Res., 5, 879-887.
    • (2006) J. Proteome Res. , vol.5 , pp. 879-887
    • Chen, J.W.1
  • 6
    • 33645753974 scopus 로고    scopus 로고
    • Conservation of intrinsic disorder in protein domains and families: II. functions of conserved disorder
    • Chen, J.W. et al. (2006b) Conservation of intrinsic disorder in protein domains and families: II. functions of conserved disorder. J. Proteome Res., 5, 888-898.
    • (2006) J. Proteome Res. , vol.5 , pp. 888-898
    • Chen, J.W.1
  • 7
    • 33846965982 scopus 로고    scopus 로고
    • Prediction of protein B-factors using multi-class bounded SVM
    • Chen, P. et al. (2007) Prediction of protein B-factors using multi-class bounded SVM. Protein Pept. Lett., 14, 185-190.
    • (2007) Protein Pept. Lett. , vol.14 , pp. 185-190
    • Chen, P.1
  • 8
    • 36749037699 scopus 로고    scopus 로고
    • Mining alpha-helix-forming molecular recognition features with cross species sequence alignments
    • Cheng, Y. et al. (2007) Mining alpha-helix-forming molecular recognition features with cross species sequence alignments. Biochemistry, 46, 13468-13477.
    • (2007) Biochemistry , vol.46 , pp. 13468-13477
    • Cheng, Y.1
  • 9
    • 33746812318 scopus 로고    scopus 로고
    • SLiMDisc: short, linear motif discovery, correcting for common evolutionary descent
    • Davey, N.E. et al. (2006) SLiMDisc: short, linear motif discovery, correcting for common evolutionary descent. Nucleic Acids Res., 34, 3546-3554.
    • (2006) Nucleic Acids Res , vol.34 , pp. 3546-3554
    • Davey, N.E.1
  • 10
    • 70349996473 scopus 로고    scopus 로고
    • ANCHOR: web server for predicting protein binding regions in disordered proteins
    • Dosztányi, Z. et al. (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
  • 11
    • 24044538903 scopus 로고    scopus 로고
    • IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content
    • Dosztányi, Z. et al. (2005) IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content. Bioinformatics, 21, 3433-3434.
    • (2005) Bioinformatics , vol.21 , pp. 3433-3434
    • Dosztányi, Z.1
  • 12
    • 50949133669 scopus 로고    scopus 로고
    • LIBLINEAR: a library for large linear classification
    • Fan, R.E. et al. (2008) LIBLINEAR: a library for large linear classification. J. Mach. Learn. Res., 9, 1871-1874.
    • (2008) J. Mach. Learn. Res. , vol.9 , pp. 1871-1874
    • Fan, R.E.1
  • 13
    • 61449123967 scopus 로고    scopus 로고
    • Improving the prediction accuracy of residue solvent accessibility and real-value backbone torsion angles of proteins by fast guidedlearning through a two-layer neural network
    • Faraggi, E. et al. (2009) Improving the prediction accuracy of residue solvent accessibility and real-value backbone torsion angles of proteins by fast guidedlearning through a two-layer neural network. Proteins, 74, 847-856.
    • (2009) Proteins , vol.74 , pp. 847-856
    • Faraggi, E.1
  • 14
    • 0002582635 scopus 로고    scopus 로고
    • Predicting binding regions within disordered proteins
    • Garner, E., et al. (1999) Predicting binding regions within disordered proteins. Genome Informatics, 10, 41-50.
    • (1999) Genome Informatics , vol.10 , pp. 41-50
    • Garner, E.1
  • 15
    • 4143107222 scopus 로고    scopus 로고
    • Analysis of ordered and disordered protein complexes reveals structural features discriminating between stable and unstable monomers
    • Gunasekaran, K. et al. (2004) Analysis of ordered and disordered protein complexes reveals structural features discriminating between stable and unstable monomers. J. Mol. Biol., 341, 1327-1341.
    • (2004) J. Mol. Biol. , vol.341 , pp. 1327-1341
    • Gunasekaran, K.1
  • 16
    • 77949601825 scopus 로고    scopus 로고
    • CD-HIT suite: a web server for clustering and comparing biological sequences
    • Huang, Y. et al. (2010) CD-HIT suite: a web server for clustering and comparing biological sequences. Bioinformatics, 26, 680-2.
    • (2010) Bioinformatics , vol.26 , pp. 680-682
    • Huang, Y.1
  • 17
    • 44349192171 scopus 로고    scopus 로고
    • Prediction of disordered regions in proteins based on the meta approach
    • Ishida, T. and Kinoshita, K. (2008) Prediction of disordered regions in proteins based on the meta approach. Bioinformatics, 24, 1344-1348.
    • (2008) Bioinformatics , vol.24 , pp. 1344-1348
    • Ishida, T.1    Kinoshita, K.2
  • 18
    • 66449084442 scopus 로고    scopus 로고
    • Infrastructure for the life sciences: design and implementation of the UniProt website
    • Jain, E. et al. (2009) Infrastructure for the life sciences: design and implementation of the UniProt website. BMC Bioinformatics, 10, 136.
    • (2009) BMC Bioinformatics , vol.10 , pp. 136
    • Jain, E.1
  • 19
    • 0036495004 scopus 로고    scopus 로고
    • Getting the most from PSI-BLAST
    • Jones, D. and Swindells, M. (2002) Getting the most from PSI-BLAST. Trends Biochem. Sci., 27, 161-164.
    • (2002) Trends Biochem. Sci. , vol.27 , pp. 161-164
    • Jones, D.1    Swindells, M.2
  • 20
    • 0031889752 scopus 로고    scopus 로고
    • Domain assignment for protein structures using a consensus approach: characterization and analysis
    • Jones, S. et al. (1998) Domain assignment for protein structures using a consensus approach: characterization and analysis. Protein Sci., 7, 233-242.
    • (1998) Protein Sci , vol.7 , pp. 233-242
    • Jones, S.1
  • 21
    • 0030028728 scopus 로고    scopus 로고
    • Principles of protein-protein interactions
    • Jones, S. and Thornton, J. (1996) Principles of protein-protein interactions. Proc. Natl Acad. Sci. USA, 93, 13-20.
    • (1996) Proc. Natl Acad. Sci. USA , vol.93 , pp. 13-20
    • Jones, S.1    Thornton, J.2
  • 22
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch, W. and Sander, C. (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22, 2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 23
    • 38549155006 scopus 로고    scopus 로고
    • AAindex: amino acid index database, progress report
    • Kawashima, S. et al. (2008) AAindex: amino acid index database, progress report. Nucleic Acids Res., 36, D202-D205.
    • (2008) Nucleic Acids Res , vol.36
    • Kawashima, S.1
  • 24
    • 80052204561 scopus 로고    scopus 로고
    • Structural protein descriptors in 1-dimension and their sequence-based predictions
    • Kurgan, L. and Disfani, F.M. (2011) Structural protein descriptors in 1-dimension and their sequence-based predictions. Curr. Protein Pept. Sci., 12, 470-489.
    • (2011) Curr. Protein Pept. Sci. , vol.12 , pp. 470-489
    • Kurgan, L.1    Disfani, F.M.2
  • 25
    • 49549111841 scopus 로고    scopus 로고
    • Intrinsic disorder prediction from the analysis of multiple protein fold recognition models
    • McGuffin, L. (2008) Intrinsic disorder prediction from the analysis of multiple protein fold recognition models. Bioinformatics, 24, 1798-1804.
    • (2008) Bioinformatics , vol.24 , pp. 1798-1804
    • McGuffin, L.1
  • 26
    • 67049119327 scopus 로고    scopus 로고
    • Prediction of protein binding regions in disordered proteins
    • Mészáros, B. et al. (2009) Prediction of protein binding regions in disordered proteins. PLoS Comput. Biol., 5, e1000376.
    • (2009) PLoS Comput. Biol. , vol.5
    • Mészáros, B.1
  • 27
    • 34547943482 scopus 로고    scopus 로고
    • Molecular principles of the interactions of disordered proteins
    • Mészáros, B. et al. (2007) Molecular principles of the interactions of disordered proteins. J. Mol. Biol., 372, 549-561.
    • (2007) J. Mol. Biol. , vol.372 , pp. 549-561
    • Mészáros, B.1
  • 28
    • 77956502766 scopus 로고    scopus 로고
    • Improved sequence-based prediction of disordered regions with multilayer fusion of multiple information sources
    • Mizianty, M.J. et al. (2010) Improved sequence-based prediction of disordered regions with multilayer fusion of multiple information sources. Bioinformatics, 26, i489-i496.
    • (2010) Bioinformatics , vol.26
    • Mizianty, M.J.1
  • 29
    • 33748456399 scopus 로고    scopus 로고
    • Analysis of molecular recognition features (MoRFs)
    • Mohan, A. et al. (2006). Analysis of molecular recognition features (MoRFs). J. Mol. Biol., 362, 1043-1059.
    • (2006) J. Mol. Biol. , vol.362 , pp. 1043-1059
    • Mohan, A.1
  • 30
    • 0015217634 scopus 로고
    • The solubility of amino acids and two glycine peptides in aqueous ethanol and dioxane solutions, Establishment of a hydrophobicity scale
    • Nozaki, Y. and Tanford, C. (1971) The solubility of amino acids and two glycine peptides in aqueous ethanol and dioxane solutions. Establishment of a hydrophobicity scale. J. Biol. Chem., 246, 2211-2217.
    • (1971) J. Biol. Chem. , vol.246 , pp. 2211-2217
    • Nozaki, Y.1    Tanford, C.2
  • 31
    • 0042622251 scopus 로고    scopus 로고
    • Scansite 2.0: Proteome-wide prediction of cell signaling interactions using short sequence motifs
    • Obenauer, J.C. et al. (2003) Scansite 2.0: Proteome-wide prediction of cell signaling interactions using short sequence motifs. Nucleic Acids Res., 31, 3635-3641.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3635-3641
    • Obenauer, J.C.1
  • 32
    • 24944546549 scopus 로고    scopus 로고
    • Coupled folding and binding with alpha-helix-forming molecular recognition elements
    • Oldfield, C.J. et al. (2005) Coupled folding and binding with alpha-helix-forming molecular recognition elements. Biochemistry, 44, 12454-12470.
    • (2005) Biochemistry , vol.44 , pp. 12454-12470
    • Oldfield, C.J.1
  • 33
    • 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.J. et al. (2008) Flexible nets: disorder and induced fit in the associations of p53 and 14-3-3 with their partners. BMC Genomics, 9(Suppl 1), S1.
    • (2008) BMC Genomics , vol.9 , Issue.SUPPL 1
    • Oldfield, C.J.1
  • 34
    • 0023989064 scopus 로고
    • Improved tools for biological sequence comparison
    • Pearson, W. and Lipman, D. (1988) Improved tools for biological sequence comparison. Proc. Natl Acad. Sci. USA, 85, 2444-8.
    • (1988) Proc. Natl Acad. Sci. USA , vol.85 , pp. 2444-2448
    • Pearson, W.1    Lipman, D.2
  • 35
    • 84857129811 scopus 로고    scopus 로고
    • Comprehensive comparative assessment of in-silico predictors of disordered regions
    • Peng, Z.L. and Kurgan, L. (2012) Comprehensive comparative assessment of in-silico predictors of disordered regions. Curr. Protein Pept. Sci., 13, 6-18.
    • (2012) Curr. Protein Pept. Sci. , vol.13 , pp. 6-18
    • Peng, Z.L.1    Kurgan, L.2
  • 36
    • 0042622252 scopus 로고    scopus 로고
    • ELM server: a new resource for investigating short functional sites in modular eukaryotic proteins
    • Puntervoll, P. et al. (2003) ELM server: a new resource for investigating short functional sites in modular eukaryotic proteins. Nucleic Acids Res., 31, 3625-3630.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3625-3630
    • Puntervoll, P.1
  • 37
    • 0034201441 scopus 로고    scopus 로고
    • EMBOSS: the European molecular biology open software suite
    • Rice, P. et al. (2000) EMBOSS: the European molecular biology open software suite. Trends Genet., 16, 276-277.
    • (2000) Trends Genet , vol.16 , pp. 276-277
    • Rice, P.1
  • 38
    • 70449441123 scopus 로고    scopus 로고
    • Epitopia: a web-server for predicting B-cell epitopes
    • Rubinstein, N.D. et al. (2009) Epitopia: a web-server for predicting B-cell epitopes. BMC Bioinformatics, 10, 287.
    • (2009) BMC Bioinformatics , vol.10 , pp. 287
    • Rubinstein, N.D.1
  • 39
    • 84885949386 scopus 로고    scopus 로고
    • Improved disorder prediction by combination of orthogonal approaches
    • Schlessinger, A. et al. (2009) Improved disorder prediction by combination of orthogonal approaches. PLoS One, 4, e4433.
    • (2009) PLoS One , vol.4
    • Schlessinger, A.1
  • 40
    • 33645288849 scopus 로고    scopus 로고
    • PROFbval: predict flexible and rigid residues in proteins
    • Schlessinger, A. et al. (2006) PROFbval: predict flexible and rigid residues in proteins. Bioinformatics, 22, 891-893.
    • (2006) Bioinformatics , vol.22 , pp. 891-893
    • Schlessinger, A.1
  • 41
    • 65249102824 scopus 로고    scopus 로고
    • Close encounters of the third kind: disordered domains and the interactions of proteins
    • Tompa, P. et al. (2009) Close encounters of the third kind: disordered domains and the interactions of proteins. Bioessays, 31, 328-335.
    • (2009) Bioessays , vol.31 , pp. 328-335
    • Tompa, P.1
  • 42
    • 77949916296 scopus 로고    scopus 로고
    • Understanding protein non-folding
    • Uversky, V.N. and Dunker, A.K. (2010) Understanding protein non-folding. Biochim Biophys Acta, 1804, 1231-1264.
    • (2010) Biochim Biophys Acta , vol.1804 , pp. 1231-1264
    • Uversky, V.N.1    Dunker, A.K.2
  • 43
    • 34250815165 scopus 로고    scopus 로고
    • Characterization of molecular recognition features, MoRFs, and their binding partners
    • Vacic, V, et al. (2007) Characterization of molecular recognition features, MoRFs, and their binding partners. J. Proteome Res., 6, 2351-2366.
    • (2007) J. Proteome Res. , vol.6 , pp. 2351-2366
    • Vacic, V.1
  • 44
    • 3242891318 scopus 로고    scopus 로고
    • The DISOPRED server for the prediction of protein disorder
    • Ward, J. et al. (2004) The DISOPRED server for the prediction of protein disorder. Bioinformatics, 20, 2138-2139.
    • (2004) Bioinformatics , vol.20 , pp. 2138-2139
    • Ward, J.1
  • 45
    • 84855184716 scopus 로고    scopus 로고
    • SPINE-D: accurate prediction of short and long disordered regions by a single neural-network based method
    • Zhang, T. et al. (2012) SPINE-D: accurate prediction of short and long disordered regions by a single neural-network based method. J. Biomol. Struct. Dyn., 29, 799-813.
    • (2012) J. Biomol. Struct. Dyn. , vol.29 , pp. 799-813
    • Zhang, T.1
  • 46
    • 0345827721 scopus 로고    scopus 로고
    • Quantifying the effect of burial of amino acid residues on protein stability
    • Zhou, H. and Zhou, Y. (2004) Quantifying the effect of burial of amino acid residues on protein stability. Proteins, 54, 315-322.
    • (2004) Proteins , vol.54 , pp. 315-322
    • Zhou, H.1    Zhou, Y.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.