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Volumn 26, Issue 3, 2009, Pages 310-318

Globally, unrelated protein sequences appear random

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EID: 77949533055     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btp660     Document Type: Article
Times cited : (13)

References (34)
  • 1
    • 33745259286 scopus 로고    scopus 로고
    • Protein secondary structure prediction for a single-sequence using hidden semi-Markov models
    • Aydin, Z. et al. (2006) Protein secondary structure prediction for a single-sequence using hidden semi-Markov models. BMC Bioinformatics, 7, 178.
    • (2006) BMC Bioinformatics , vol.7 , pp. 178
    • Aydin, Z.1
  • 2
    • 0032972986 scopus 로고    scopus 로고
    • Is protein folding hierarchic? i. local structure and peptide folding
    • Baldwin, R. and Rose,G. (1999) Is protein folding hierarchic? i. local structure and peptide folding. Trends Biochem. Sci., 24, 26-33.
    • (1999) Trends Biochem. Sci. , vol.24 , pp. 26-33
    • Baldwin, R.1    Rose, G.2
  • 3
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: a practical and powerful approach to multiple testing
    • Benjamini, Y. and Hochberg, Y. (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B (Methodol.), 57, 289-300.
    • (1995) J. R. Stat. Soc. Ser. B (Methodol.) , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 4
    • 0032568596 scopus 로고    scopus 로고
    • Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships
    • Brenner, S.E. et al. (1998) Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships. Proc. Natl Acad. Sci. USA, 95, 6073-6078.
    • (1998) Proc. Natl Acad. Sci. USA , vol.95 , pp. 6073-6078
    • Brenner, S.E.1
  • 5
    • 0015967881 scopus 로고
    • Conformational parameters for amino acids in helical, beta-sheet, and random coil regions calculated from proteins
    • Chou, P.Y. and Fasman,G.D. (1974) Conformational parameters for amino acids in helical, beta-sheet, and random coil regions calculated from proteins. Biochemistry, 13, 211-22.
    • (1974) Biochemistry , vol.13 , pp. 211-222
    • Chou, P.Y.1    Fasman, G.D.2
  • 6
    • 3543145933 scopus 로고    scopus 로고
    • Protein secondary structure: entropy, correlations and prediction
    • Crooks, G.E. and Brenner, S.E. (2004) Protein secondary structure: entropy, correlations and prediction. Bioinformatics, 20, 1603-11.
    • (2004) Bioinformatics , vol.20 , pp. 1603-1611
    • Crooks, G.E.1    Brenner, S.E.2
  • 7
    • 36749055649 scopus 로고    scopus 로고
    • Structure prediction for casp7 targets using extensive all-atom refinement with rosetta@home
    • Das, R. et al. (2007) Structure prediction for casp7 targets using extensive all-atom refinement with rosetta@home. Proteins, 69 (Suppl. 8), 118-128.
    • (2007) Proteins , vol.69 , Issue.SUPPL. 8 , pp. 118-128
    • Das, R.1
  • 8
    • 0031743421 scopus 로고    scopus 로고
    • Profile hidden Markov models
    • Eddy, S.R. (1998) Profile hidden Markov models. Bioinformatics, 14, 755-763.
    • (1998) Bioinformatics , vol.14 , pp. 755-763
    • Eddy, S.R.1
  • 9
    • 0001514262 scopus 로고
    • Statistics of local complexity in amino acid sequences and sequence databases
    • Federhen, J.C.W.S. (1993) Statistics of local complexity in amino acid sequences and sequence databases. Comput. Chem., 17, 149-163.
    • (1993) Comput. Chem. , vol.17 , pp. 149-163
    • Federhen, J.C.W.S.1
  • 10
    • 0028856785 scopus 로고
    • Optimization of rates of protein folding: the nucleation-condensation mechanism and its implications
    • Fersht, A.R. (1995) Optimization of rates of protein folding: the nucleation-condensation mechanism and its implications. Proc. Natl. Acad. Sci. USA, 92, 10869-10873.
    • (1995) Proc. Natl. Acad. Sci. USA , vol.92 , pp. 10869-10873
    • Fersht, A.R.1
  • 11
    • 0026345750 scopus 로고
    • Folding of chymotrypsin inhibitor 2.1. evidence for a two-state transition
    • Jackson, S.E. and Fersht, A.R. (1991) Folding of chymotrypsin inhibitor 2.1. evidence for a two-state transition. Biochemistry, 30, 10428-10435.
    • (1991) Biochemistry , vol.30 , pp. 10428-10435
    • Jackson, S.E.1    Fersht, A.R.2
  • 12
    • 36749086922 scopus 로고    scopus 로고
    • Assessment of CASP7 structure predictions for template free targets
    • Jauch, R. et al. (2007) Assessment of CASP7 structure predictions for template free targets. Proteins, 69 (Suppl. 8), 57-67.
    • (2007) Proteins , vol.69 , Issue.SUPPL. 8 , pp. 57-67
    • Jauch, R.1
  • 13
    • 0033578684 scopus 로고    scopus 로고
    • Protein secondary structure prediction based on position-specific scoring matrices
    • Jones, D. (1999) Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol., 292, 195-202.
    • (1999) J. Mol. Biol. , vol.292 , pp. 195-202
    • Jones, D.1
  • 14
    • 0028327236 scopus 로고
    • Protein folding dynamics: the diffusion-collision model and experimental data
    • Karplus, M. and Weaver, D.L. (1994) Protein folding dynamics: the diffusion-collision model and experimental data. Protein Sci., 3, 650-668.
    • (1994) Protein Sci. , vol.3 , pp. 650-668
    • Karplus, M.1    Weaver, D.L.2
  • 15
    • 0037456298 scopus 로고    scopus 로고
    • The complete folding pathway of a protein from nanoseconds to microseconds
    • Mayor, U. et al. (2003) The complete folding pathway of a protein from nanoseconds to microseconds. Nature, 421, 863-867.
    • (2003) Nature , vol.421 , pp. 863-867
    • Mayor, U.1
  • 16
    • 17444397116 scopus 로고    scopus 로고
    • Porter: a new, accurate server for protein secondary structure prediction
    • McLysaght, G.P.A. (2005) Porter: a new, accurate server for protein secondary structure prediction. Bioinformatics, 21, 1719-1720.
    • (2005) Bioinformatics , vol.21 , pp. 1719-1720
    • McLysaght, G.P.A.1
  • 17
    • 0035957514 scopus 로고    scopus 로고
    • Evolutionary conservation of the folding nucleus
    • Mirny, L. and Shakhnovich,E. (2001). Evolutionary conservation of the folding nucleus. J. Mol. Biol., 308, 123-129.
    • (2001) J. Mol. Biol. , vol.308 , pp. 123-129
    • Mirny, L.1    Shakhnovich, E.2
  • 18
    • 20444484434 scopus 로고    scopus 로고
    • A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction
    • Moult, J. (2005) A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction. Curr. Opin. Struct. Biol., 15, 285-289.
    • (2005) Curr. Opin. Struct. Biol. , vol.15 , pp. 285-289
    • Moult, J.1
  • 19
    • 0001338954 scopus 로고    scopus 로고
    • Simplified amino acid alphabets for protein fold recognition and implications for folding
    • Murphy, L.R. et al. (2000) Simplified amino acid alphabets for protein fold recognition and implications for folding. Protein Eng., 13, 149-152.
    • (2000) Protein Eng. , vol.13 , pp. 149-152
    • Murphy, L.R.1
  • 20
    • 33750243061 scopus 로고    scopus 로고
    • Numerical solutions for patterns statistics on markov chains
    • Nuel, G. (2006) Numerical solutions for patterns statistics on markov chains. Stat. Appl. Genet. Mol. Biol., 5, Article 26.
    • (2006) Stat. Appl. Genet. Mol. Biol. , vol.5
    • Nuel, G.1
  • 21
    • 0030777303 scopus 로고    scopus 로고
    • CATH-a hierarchic classification of protein domain structures
    • Orengo, C. et al. (1997) CATH-a hierarchic classification of protein domain structures. Structure, 5, 1093-108.
    • (1997) Structure , vol.5 , pp. 1093-1108
    • Orengo, C.1
  • 22
    • 20444449200 scopus 로고    scopus 로고
    • The limits of protein sequence comparison?
    • Pearson, W.R. and Sierk,M.L. (2005) The limits of protein sequence comparison? Curr. Opin. Struct. Biol., 15, 254-260.
    • (2005) Curr. Opin. Struct. Biol. , vol.15 , pp. 254-260
    • Pearson, W.R.1    Sierk, M.L.2
  • 23
    • 0348047627 scopus 로고    scopus 로고
    • Proteomic signatures: amino acid and oligopeptide compositions differentiate among phyla
    • Pe'er, I. et al. (2004) Proteomic signatures: amino acid and oligopeptide compositions differentiate among phyla. Proteins, 54, 20-40.
    • (2004) Proteins , vol.54 , pp. 20-40
    • Pe'er, I.1
  • 24
    • 0036568279 scopus 로고    scopus 로고
    • Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles
    • Pollastri, G. et al. (2002) Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles. Proteins, 47, 228-235.
    • (2002) Proteins , vol.47 , pp. 228-235
    • Pollastri, G.1
  • 25
    • 0032496419 scopus 로고    scopus 로고
    • Protein folding and protein evolution: common folding nucleus in different subfamilies of c-type cytochromes?
    • Ptitsyn, O. (1998) Protein folding and protein evolution: common folding nucleus in different subfamilies of c-type cytochromes? J. Mol. Biol., 278, 655-666.
    • (1998) J. Mol. Biol. , vol.278 , pp. 655-666
    • Ptitsyn, O.1
  • 26
    • 0022554080 scopus 로고
    • Protein structure and neutral theory of evolution
    • Ptitsyn, O. and Volkenstein, M. (1986) Protein structure and neutral theory of evolution. J. Biomol. Struct. Dyn., 4, 137-156.
    • (1986) J. Biomol. Struct. Dyn. , vol.4 , pp. 137-156
    • Ptitsyn, O.1    Volkenstein, M.2
  • 27
    • 0034125366 scopus 로고    scopus 로고
    • Probabilistic and statistical properties of words: an overview
    • Reinert, G. et al. (2000) Probabilistic and statistical properties of words: an overview. J. Comput. Biol., 7, 1-46.
    • (2000) J. Comput. Biol. , vol.7 , pp. 1-46
    • Reinert, G.1
  • 28
    • 1642464839 scopus 로고    scopus 로고
    • Protein structure prediction using Rosetta
    • Rohl, C.A. et al. (2004) Protein structure prediction using Rosetta. Methods Enzymol., 383, 66-93.
    • (2004) Methods Enzymol. , vol.383 , pp. 66-93
    • Rohl, C.A.1
  • 29
    • 0035782925 scopus 로고    scopus 로고
    • Review: protein secondary structure prediction continues to rise
    • Rost, B. (2001) Review: protein secondary structure prediction continues to rise. J. Struct. Biol., 134, 204-218.
    • (2001) J. Struct. Biol. , vol.134 , pp. 204-218
    • Rost, B.1
  • 30
    • 0027169638 scopus 로고
    • Improved prediction of protein secondary structure by use of sequence profiles and neural networks
    • Rost, B. and Sander,C. (1993) Improved prediction of protein secondary structure by use of sequence profiles and neural networks. Proc. Natl. Acad. Sci. USA, 90, 7558-7562.
    • (1993) Proc. Natl. Acad. Sci. USA , vol.90 , pp. 7558-7562
    • Rost, B.1    Sander, C.2
  • 31
    • 0030925920 scopus 로고    scopus 로고
    • Pfam: a comprehensive database of protein domain families based on seed alignments
    • Sonnhammer, E. et al. (1997) Pfam: a comprehensive database of protein domain families based on seed alignments. Proteins, 28, 405-420.
    • (1997) Proteins , vol.28 , pp. 405-420
    • Sonnhammer, E.1
  • 32
    • 0042424602 scopus 로고    scopus 로고
    • Statistical significance for genomewide studies
    • Storey, J.D. and Tibshirani, R. (2003) Statistical significance for genomewide studies. Proc. Natl Acad. Sci. USA, 100, 9440-9445.
    • (2003) Proc. Natl Acad. Sci. USA , vol.100 , pp. 9440-9445
    • Storey, J.D.1    Tibshirani, R.2
  • 33
    • 0034619248 scopus 로고    scopus 로고
    • Information content of protein sequences
    • Weiss, O. et al. (2000) Information content of protein sequences. J. Theor Biol., 206, 379-86.
    • (2000) J. Theor Biol. , vol.206 , pp. 379-386
    • Weiss, O.1
  • 34
    • 0030309937 scopus 로고    scopus 로고
    • Motif identification neural design for rapid and sensitive protein family search
    • Wu, C.H. et al. (1996) Motif identification neural design for rapid and sensitive protein family search. Pac. Symp. Biocomput., 674-685.
    • (1996) Pac. Symp. Biocomput. , pp. 674-685
    • Wu, C.H.1


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