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Volumn 14, Issue 8, 1998, Pages 707-714

Measurement of the effectiveness of transitive sequence comparison, through a third 'intermediate' sequence

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; COMPARATIVE STUDY; GENETIC LINKAGE; PRIORITY JOURNAL; STATISTICAL ANALYSIS;

EID: 0031762837     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/14.8.707     Document Type: Article
Times cited : (51)

References (52)
  • 1
    • 0031576355 scopus 로고    scopus 로고
    • Do aligned sequences share the same fold?
    • Abagyan, R.A. and Batalov, S. (1997) Do aligned sequences share the same fold? J Mol. Biol., 273, 355-368.
    • (1997) J Mol. Biol. , vol.273 , pp. 355-368
    • Abagyan, R.A.1    Batalov, S.2
  • 6
    • 0025234646 scopus 로고
    • Construction of validated, non-redundant composite protein sequence databases
    • Bleasby, A.J. and Wootton, J.C. (1990) Construction of validated, non-redundant composite protein sequence databases. Protein Eng., 3, 153-159.
    • (1990) Protein Eng. , vol.3 , pp. 153-159
    • Bleasby, A.J.1    Wootton, J.C.2
  • 7
    • 0028050261 scopus 로고
    • OWL - A non-redundant composite protein sequence database
    • Bleasby, A.J., Akrigg, D. and Attwood, T.K. (1994) OWL - a non-redundant composite protein sequence database. Nucleic Acids Res., 22, 3574-3577.
    • (1994) Nucleic Acids Res. , vol.22 , pp. 3574-3577
    • Bleasby, A.J.1    Akrigg, D.2    Attwood, T.K.3
  • 8
    • 0025830469 scopus 로고
    • A method to identify protein sequences that fold into a known three-dimensional structure
    • Bowie, J.U., Luthy, R. and Eisenberg, D. (1991) A method to identify protein sequences that fold into a known three-dimensional structure. Science (Washington), 253, 164-170.
    • (1991) Science (Washington) , vol.253 , pp. 164-170
    • Bowie, J.U.1    Luthy, R.2    Eisenberg, D.3
  • 11
    • 0030983386 scopus 로고    scopus 로고
    • Population statistics of protein structures: Lessons from structural classifications
    • Brenner, S.E., Chothia, C. and Hubbard, T.J. (1997) Population statistics of protein structures: lessons from structural classifications. Curr. Opin. Struct. Biol., 7, 369-376.
    • (1997) Curr. Opin. Struct. Biol. , vol.7 , pp. 369-376
    • Brenner, S.E.1    Chothia, C.2    Hubbard, T.J.3
  • 13
    • 0027318317 scopus 로고
    • An empirical energy function for threading protein sequence through the folding motif
    • Bryant, S.H. and Lawrence, C.E. (1993) An empirical energy function for threading protein sequence through the folding motif. Proteins Struct. Funct. Genet., 16, 92-112.
    • (1993) Proteins Struct. Funct. Genet. , vol.16 , pp. 92-112
    • Bryant, S.H.1    Lawrence, C.E.2
  • 14
    • 0031020765 scopus 로고    scopus 로고
    • How far can sequences diverge?
    • Chothia, C. and Gerstein, M. (1997) How far can sequences diverge? Nature, 385, 579-581.
    • (1997) Nature , vol.385 , pp. 579-581
    • Chothia, C.1    Gerstein, M.2
  • 15
    • 0022706389 scopus 로고
    • The relation between the divergence of sequence and structure in proteins
    • Chothia, C. and Lesk, A.M. (1986) The relation between the divergence of sequence and structure in proteins. EMBO J., 5, 823-826.
    • (1986) EMBO J. , vol.5 , pp. 823-826
    • Chothia, C.1    Lesk, A.M.2
  • 18
    • 0029259085 scopus 로고
    • Maximum discrimination hidden Markov models of sequence consensus
    • Eddy, S.R., Mitchison, G. and Durbin, R. (1994) Maximum discrimination hidden Markov models of sequence consensus. J. Comput. Biol., 9, 9-23.
    • (1994) J. Comput. Biol. , vol.9 , pp. 9-23
    • Eddy, S.R.1    Mitchison, G.2    Durbin, R.3
  • 19
    • 0031565915 scopus 로고    scopus 로고
    • A structural census of genomes: Comparing eukaryotic, bacterial and archaeal genomes in terms of protein structure
    • Gerstein, M. (1997) A structural census of genomes: comparing eukaryotic, bacterial and archaeal genomes in terms of protein structure. J. Mol. Biol., 274, 562-576.
    • (1997) J. Mol. Biol. , vol.274 , pp. 562-576
    • Gerstein, M.1
  • 21
    • 0031938039 scopus 로고    scopus 로고
    • Comprehensive assessment of automatic structural alignment against a manual standard, the scop classification of proteins
    • Gerstein, M. and Levitt, M. (1998) Comprehensive assessment of automatic structural alignment against a manual standard, the scop classification of proteins. Protein Sci., 7, 445-456.
    • (1998) Protein Sci. , vol.7 , pp. 445-456
    • Gerstein, M.1    Levitt, M.2
  • 23
    • 0028205447 scopus 로고
    • Enlarged representative set of protein structures
    • Hobohm, U. and Sander, C. (1994) Enlarged representative set of protein structures. Protein Sci., 3, 522.
    • (1994) Protein Sci. , vol.3 , pp. 522
    • Hobohm, U.1    Sander, C.2
  • 24
  • 25
    • 0030902463 scopus 로고    scopus 로고
    • New horizons in sequence analysis
    • Hubbard, T.J. (1997) New horizons in sequence analysis. Curr. Opin. Struct. Biol., 7, 190-193.
    • (1997) Curr. Opin. Struct. Biol. , vol.7 , pp. 190-193
    • Hubbard, T.J.1
  • 27
    • 0027305858 scopus 로고
    • Alignment and searching for common protein folds using a databank of structural templates
    • Johnson, M.S., Overington, J.P. and Blundell, T.L. (1993) Alignment and searching for common protein folds using a databank of structural templates. J. Mol. Biol., 231, 735-752.
    • (1993) J. Mol. Biol. , vol.231 , pp. 735-752
    • Johnson, M.S.1    Overington, J.P.2    Blundell, T.L.3
  • 28
  • 29
    • 0026690571 scopus 로고
    • A new approach to protein fold recognition
    • Jones, D.T., Taylor, W.R. and Thornton, J.M. (1992) A new approach to protein fold recognition. Nature, 358, 86-89.
    • (1992) Nature , vol.358 , pp. 86-89
    • Jones, D.T.1    Taylor, W.R.2    Thornton, J.M.3
  • 30
    • 0027175241 scopus 로고
    • Applications and statistics for multiple high-scoring segments in molecular sequences
    • Karlin, S. and Altschul, S.F. (1993) Applications and statistics for multiple high-scoring segments in molecular sequences. Proc. Natl Acad. Sci. USA, 90, 5873-5877.
    • (1993) Proc. Natl Acad. Sci. USA , vol.90 , pp. 5873-5877
    • Karlin, S.1    Altschul, S.F.2
  • 31
    • 0028181441 scopus 로고
    • Hidden Markov models in computational biology: Applications to protein modelling
    • Krogh, A., Brown, M., Mian, I.S., Sjölander, K. and Haussler, D. (1994) Hidden Markov models in computational biology: applications to protein modelling. J. Mol. Biol., 235, 1501-1531.
    • (1994) J. Mol. Biol. , vol.235 , pp. 1501-1531
    • Krogh, A.1    Brown, M.2    Mian, I.S.3    Sjölander, K.4    Haussler, D.5
  • 32
    • 0032568649 scopus 로고    scopus 로고
    • A unified statistical framework for sequence comparison and structure comparison
    • Levitt, M. and Gerstein, M. (1998) A unified statistical framework for sequence comparison and structure comparison. Proc. Natl Acad. Sci. USA, 95, 5913-5920.
    • (1998) Proc. Natl Acad. Sci. USA , vol.95 , pp. 5913-5920
    • Levitt, M.1    Gerstein, M.2
  • 33
    • 0021919480 scopus 로고
    • Rapid and sensitive protein similarity searches
    • Lipman, D.J. and Pearson, W.R. (1985) Rapid and sensitive protein similarity searches. Science, 227, 1435-1441.
    • (1985) Science , vol.227 , pp. 1435-1441
    • Lipman, D.J.1    Pearson, W.R.2
  • 34
    • 0014935646 scopus 로고
    • Natural selection and the concept of a protein space
    • Maynard Smith, J. (1970) Natural selection and the concept of a protein space. Nature, 225, 563-564.
    • (1970) Nature , vol.225 , pp. 563-564
    • Maynard Smith, J.1
  • 35
    • 0028961335 scopus 로고
    • SCOP: A structural classification of proteins for the investigation of sequences and structures
    • Murzin, A., Brenner, S.E., Hubbard, T. and Chothia, C. (1995) SCOP: a structural classification of proteins for the investigation of sequences and structures. J. Mol. Biol., 247, 536-540.
    • (1995) J. Mol. Biol. , vol.247 , pp. 536-540
    • Murzin, A.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4
  • 36
    • 0028593509 scopus 로고
    • Protein superfamilies and domain superfolds
    • Orengo, C.A., Jones, D.T. and Thornton, J.M. (1994) Protein superfamilies and domain superfolds. Nature, 372, 631-634.
    • (1994) Nature , vol.372 , pp. 631-634
    • Orengo, C.A.1    Jones, D.T.2    Thornton, J.M.3
  • 37
    • 0031576361 scopus 로고    scopus 로고
    • Intermediate sequences increase the detection of homology between sequences
    • Park, J., Teichmann, S.A., Hubbard, T. and Chothia, C. (1997) Intermediate sequences increase the detection of homology between sequences. J. Mol. Biol., 273, 349-354.
    • (1997) J. Mol. Biol. , vol.273 , pp. 349-354
    • Park, J.1    Teichmann, S.A.2    Hubbard, T.3    Chothia, C.4
  • 38
    • 0029933671 scopus 로고    scopus 로고
    • Effective protein sequence comparison
    • Pearson, W.R. (1996) Effective protein sequence comparison. Methods Enzymol., 266, 227-259.
    • (1996) Methods Enzymol. , vol.266 , pp. 227-259
    • Pearson, W.R.1
  • 39
    • 0030776390 scopus 로고    scopus 로고
    • Identifying distantly related protein sequences
    • Pearson, W.R. (1997) Identifying distantly related protein sequences. Comput. Applic. Biosci., 13, 325-332.
    • (1997) Comput. Applic. Biosci. , vol.13 , pp. 325-332
    • Pearson, W.R.1
  • 40
    • 0032512799 scopus 로고    scopus 로고
    • Empirical statistical estimates for sequence similarity searches
    • Pearson, W.R. (1998) Empirical statistical estimates for sequence similarity searches. J. Mol. Biol., 276, 71-84.
    • (1998) J. Mol. Biol. , vol.276 , pp. 71-84
    • Pearson, W.R.1
  • 41
    • 0023989064 scopus 로고
    • Improved tools for biological sequence analysis
    • Pearson, W.R. and Lipman, D.J. (1988) Improved tools for biological sequence analysis. Proc. Natl Acad. Sci. USA, 85, 2444-2448.
    • (1988) Proc. Natl Acad. Sci. USA , vol.85 , pp. 2444-2448
    • Pearson, W.R.1    Lipman, D.J.2
  • 42
    • 0031573415 scopus 로고    scopus 로고
    • Comparison of DNA sequences with protein sequences
    • Pearson, W.R., Wood, T., Zhang, Z. and Miller, W. (1997) Comparison of DNA sequences with protein sequences. Genomics, 46, 24-36.
    • (1997) Genomics , vol.46 , pp. 24-36
    • Pearson, W.R.1    Wood, T.2    Zhang, Z.3    Miller, W.4
  • 43
    • 0019887799 scopus 로고
    • Identification of common molecular subsequences
    • Smith, T.F. and Waterman, M.S. (1981) Identification of common molecular subsequences. J. Mol. Biol., 147, 195-197.
    • (1981) J. Mol. Biol. , vol.147 , pp. 195-197
    • Smith, T.F.1    Waterman, M.S.2
  • 44
    • 0030925920 scopus 로고    scopus 로고
    • Pfam: A comprehensive database of protein domain families based on seed alignments
    • in press
    • Sonnhammer, J.E., Eddy, S. and Durbin, R. (1997) Pfam: a comprehensive database of protein domain families based on seed alignments. Proteins, in press.
    • (1997) Proteins
    • Sonnhammer, J.E.1    Eddy, S.2    Durbin, R.3
  • 45
    • 0029637588 scopus 로고
    • PDBbrowse - A graphics interface to the Brookhaven Protein Data Bank
    • Stampf, D.R., Felder, C.E. and Sussman, J.L. (1995) PDBbrowse - a graphics interface to the Brookhaven Protein Data Bank. Nature, 374, 572-574.
    • (1995) Nature , vol.374 , pp. 572-574
    • Stampf, D.R.1    Felder, C.E.2    Sussman, J.L.3
  • 46
    • 0028091659 scopus 로고
    • Detection of conserved segments in proteins: Iterative scanning of sequence databases with alignment blocks
    • Tatusov, R.L., Altschul, S.F. and Koonin, E.V. (1994) Detection of conserved segments in proteins: iterative scanning of sequence databases with alignment blocks. Proc. Natl Acad. Sci. USA, 91, 12091-12095.
    • (1994) Proc. Natl Acad. Sci. USA , vol.91 , pp. 12091-12095
    • Tatusov, R.L.1    Altschul, S.F.2    Koonin, E.V.3
  • 47
    • 0027496980 scopus 로고
    • Weighting in sequence space: A comparison of methods in terms of generalized sequences
    • Vingron, M. and Sibbald, P.R. (1993) Weighting in sequence space: A comparison of methods in terms of generalized sequences. Proc. Natl Acad. Sci. USA, 90, 8777-8781.
    • (1993) Proc. Natl Acad. Sci. USA , vol.90 , pp. 8777-8781
    • Vingron, M.1    Sibbald, P.R.2
  • 49
    • 0030987407 scopus 로고    scopus 로고
    • MultiCoil: A program for predicting two- and three-stranded coiled coils
    • Wolf, E., Kim, P.S. and Berger, B. (1997) MultiCoil: a program for predicting two- and three-stranded coiled coils. Protein Sci., 6, 1179-1189.
    • (1997) Protein Sci. , vol.6 , pp. 1179-1189
    • Wolf, E.1    Kim, P.S.2    Berger, B.3
  • 50
    • 0001514262 scopus 로고
    • Statistics of local complexity in amino acid sequences and sequence databases
    • Wootton, J.C. and Federhen, 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
    • Wootton, J.C.1    Federhen, S.2
  • 51
    • 0027994453 scopus 로고
    • Recognition of related proteins by iterative template refinement (itr)
    • Yi, T.M. and Lander, E.S. (1994) Recognition of related proteins by iterative template refinement (itr). Protein Sci., 3, 1315-1328.
    • (1994) Protein Sci. , vol.3 , pp. 1315-1328
    • Yi, T.M.1    Lander, E.S.2
  • 52
    • 0029977032 scopus 로고    scopus 로고
    • Iterative template refinement: Protein-fold prediction using iterative search and hybrid sequence/structure templates
    • Yi, T. and Lander, E.S. (1996) Iterative template refinement: protein-fold prediction using iterative search and hybrid sequence/structure templates. Methods Enzymol., 266, 322-339.
    • (1996) Methods Enzymol. , vol.266 , pp. 322-339
    • Yi, T.1    Lander, E.S.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.