메뉴 건너뛰기




Volumn 31, Issue 2, 2003, Pages 683-689

Finding weak similarities between proteins by sequence profile comparison

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; LYASE; OROTIDINE 5' PHOSPHATE DECARBOXYLASE; RIBULOSE PHOSPHATE;

EID: 0037440190     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkg154     Document Type: Review
Times cited : (56)

References (44)
  • 1
    • 0023989064 scopus 로고
    • Improved tools for biological sequence comparison
    • Pearson,W.R. and Lipman,D.J. (1988) Improved tools for biological sequence comparison. 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
  • 3
    • 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
  • 4
    • 0032940341 scopus 로고    scopus 로고
    • Combining sensitive database searches with multiple intermediates to detect distant homologues
    • Salamov,A.A., Suwa,M., Orengo,C.A. and Swindells,M.B. (1999) Combining sensitive database searches with multiple intermediates to detect distant homologues. Protein Eng., 12, 95-100.
    • (1999) Protein Eng. , vol.12 , pp. 95-100
    • Salamov, A.A.1    Suwa, M.2    Orengo, C.A.3    Swindells, M.B.4
  • 7
    • 0029887381 scopus 로고    scopus 로고
    • Hidden Markov models for sequence analysis: Extension and analysis of the basic method
    • Hughey,R. and Krogh,A. (1996) Hidden Markov models for sequence analysis: extension and analysis of the basic method. Comput. Appl. Biosci., 12, 95-107.
    • (1996) Comput. Appl. Biosci. , vol.12 , pp. 95-107
    • Hughey, R.1    Krogh, A.2
  • 10
    • 0030788541 scopus 로고    scopus 로고
    • Extracting protein alignment models from the sequence database
    • Neuwald,A.F., Liu,J.S., Lipman,D.J. and Lawrence,C.E. (1997) Extracting protein alignment models from the sequence database. Nucleic Acids Res., 25, 1665-1677.
    • (1997) Nucleic Acids Res. , vol.25 , pp. 1665-1677
    • Neuwald, A.F.1    Liu, J.S.2    Lipman, D.J.3    Lawrence, C.E.4
  • 11
    • 0032509105 scopus 로고    scopus 로고
    • Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods
    • Park,J., Karplus,K., Barrett,C., Hughey,R., Haussler,D., Hubbard,T. and Chothia,C. (1998) Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods. J. Mol. Biol., 284, 1201-1210.
    • (1998) J. Mol. Biol. , vol.284 , pp. 1201-1210
    • Park, J.1    Karplus, K.2    Barrett, C.3    Hughey, R.4    Haussler, D.5    Hubbard, T.6    Chothia, C.7
  • 12
    • 0027210418 scopus 로고
    • Optimal alignment between groups of sequences and its application to multiple sequence alignment
    • Gotoh,O. (1993) Optimal alignment between groups of sequences and its application to multiple sequence alignment. Comput. Appl. Biosci., 9, 361-370.
    • (1993) Comput. Appl. Biosci. , vol.9 , pp. 361-370
    • Gotoh, O.1
  • 13
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice Nucleic
    • Thompson,J.D., Higgins,D.G. and Gibson,T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.
    • (1994) Acids Res. , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 14
    • 0029789461 scopus 로고    scopus 로고
    • Searching databases of conserved sequence regions by aligning protein multiple-alignments
    • Pietrokovski,S. (1996) Searching databases of conserved sequence regions by aligning protein multiple-alignments. Nucleic Acids Res., 24, 3836-3845.
    • (1996) Nucleic Acids Res. , vol.24 , pp. 3836-3845
    • Pietrokovski, S.1
  • 16
    • 0033997036 scopus 로고    scopus 로고
    • Comparison of sequence profiles. Strategies for structural predictions using sequence information
    • Rychlewski,L., Jaroszewski,L., Li,W. and Godzik,A. (2000) Comparison of sequence profiles. Strategies for structural predictions using sequence information. Protein Sci., 9, 232-241.
    • (2000) Protein Sci. , vol.9 , pp. 232-241
    • Rychlewski, L.1    Jaroszewski, L.2    Li, W.3    Godzik, A.4
  • 17
    • 0036307493 scopus 로고    scopus 로고
    • Within the twilight zone: A sensitive profile-profile comparison tool based on information theory
    • Yona,G. and Levitt,M. (2002) Within the twilight zone: a sensitive profile-profile comparison tool based on information theory. J. Mol. Biol., 315, 1257-1275.
    • (2002) J. Mol. Biol. , vol.315 , pp. 1257-1275
    • Yona, G.1    Levitt, M.2
  • 18
    • 0344417226 scopus 로고    scopus 로고
    • The Helicobacter pylori genome: From sequence analysis to structural and functional predictions
    • Pawlowski,K., Zhang,B., Rychlewski,L. and Godzik,A. (1999) The Helicobacter pylori genome: from sequence analysis to structural and functional predictions. Proteins, 36, 20-30.
    • (1999) Proteins , vol.36 , pp. 20-30
    • Pawlowski, K.1    Zhang, B.2    Rychlewski, L.3    Godzik, A.4
  • 19
  • 21
    • 0033120222 scopus 로고    scopus 로고
    • Identification of homologous core structures
    • Matsuo,Y. and Bryant,S.H. (1999) Identification of homologous core structures. Proteins, 35, 70-79.
    • (1999) Proteins , vol.35 , pp. 70-79
    • Matsuo, Y.1    Bryant, S.H.2
  • 22
    • 0028290005 scopus 로고
    • Parser for protein folding units
    • Holm,L. and Sander,C. (1994) Parser for protein folding units. Proteins, 19, 256-268.
    • (1994) Proteins , vol.19 , pp. 256-268
    • Holm, L.1    Sander, C.2
  • 25
    • 0028838717 scopus 로고
    • Threading a database of protein cores
    • Madej,T., Gibrat,J.F. and Bryant,S.H. (1995) Threading a database of protein cores. Proteins, 23, 356-369.
    • (1995) Proteins , vol.23 , pp. 356-369
    • Madej, T.1    Gibrat, J.F.2    Bryant, S.H.3
  • 26
    • 0028961335 scopus 로고
    • SCOP: A structural classification of proteins database for the investigation of sequences and structures
    • Murzin,A.G., Brenner,S.E., Hubbard,T. and Chothia,C. (1995) SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol., 247, 536-540.
    • (1995) J. Mol. Biol. , vol.247 , pp. 536-540
    • Murzin, A.G.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4
  • 27
    • 0029974002 scopus 로고    scopus 로고
    • Evaluation of threading specificity and accuracy
    • Bryant,S.H. (1996) Evaluation of threading specificity and accuracy. Proteins, 26, 172-185.
    • (1996) Proteins , vol.26 , pp. 172-185
    • Bryant, S.H.1
  • 28
    • 0034628922 scopus 로고    scopus 로고
    • Combination of threading potentials and sequence profiles improves fold recognition
    • Panchenko,A.R., Marchler-Bauer,A. and Bryant,S.H. (2000) Combination of threading potentials and sequence profiles improves fold recognition. J. Mol. Biol., 296, 1319-1331.
    • (2000) J. Mol. Biol. , vol.296 , pp. 1319-1331
    • Panchenko, A.R.1    Marchler-Bauer, A.2    Bryant, S.H.3
  • 29
    • 0001969211 scopus 로고    scopus 로고
    • Use of receiver operating characteristic (ROC) analysis to evaluate sequence matching
    • Gribskov,M. and Robinson,N.L. (1996) Use of receiver operating characteristic (ROC) analysis to evaluate sequence matching. Comput. Chem., 20, 25-33.
    • (1996) Comput. Chem. , vol.20 , pp. 25-33
    • Gribskov, M.1    Robinson, N.L.2
  • 31
    • 0031296896 scopus 로고    scopus 로고
    • Measures of threading specificity and accuracy
    • Marchler-Bauer,A. and Bryant,S.H. (1997) Measures of threading specificity and accuracy. Proteins, (suppl. 1), 74-82.
    • (1997) Proteins , Issue.SUPPL. 1 , pp. 74-82
    • Marchler-Bauer, A.1    Bryant, S.H.2
  • 32
    • 0031307020 scopus 로고    scopus 로고
    • Competitive assessment of protein fold recognition and alignment accuracy
    • Levitt,M. (1997) Competitive assessment of protein fold recognition and alignment accuracy. Proteins, (suppl. 1), 92-104.
    • (1997) Proteins , Issue.SUPPL. 1 , pp. 92-104
    • Levitt, M.1
  • 33
    • 0032606039 scopus 로고    scopus 로고
    • Critical assessment of methods of protein structure prediction (CASP): Round III
    • Moult,J., Hubbard,T., Fidelis,K. and Pedersen,J.T. (1999) Critical assessment of methods of protein structure prediction (CASP): round III. Proteins, (suppl. 3), 2-6.
    • (1999) Proteins , Issue.SUPPL. 3 , pp. 2-6
    • Moult, J.1    Hubbard, T.2    Fidelis, K.3    Pedersen, J.T.4
  • 34
    • 0031303337 scopus 로고    scopus 로고
    • A retrospective analysis of CASP2 threading predictions
    • Marchler-Bauer,A., Levitt,M. and Bryant,S.H. (1997) A retrospective analysis of CASP2 threading predictions. Proteins, (suppl. 1), 83-91.
    • (1997) Proteins , Issue.SUPPL. 1 , pp. 83-91
    • Marchler-Bauer, A.1    Levitt, M.2    Bryant, S.H.3
  • 35
    • 0032613429 scopus 로고    scopus 로고
    • Threading with explicit models for evolutionary conservation of structure and sequence
    • Panchenko,A., Marchler-Bauer,A. and Bryant,S.H. (1999) Threading with explicit models for evolutionary conservation of structure and sequence. Proteins, 37, 133-140.
    • (1999) Proteins , vol.37 , pp. 133-140
    • Panchenko, A.1    Marchler-Bauer, A.2    Bryant, S.H.3
  • 37
    • 0032568596 scopus 로고    scopus 로고
    • Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships
    • Brenner,S.E., Chothia,C. and Hubbard,T.J. (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    Chothia, C.2    Hubbard, T.J.3
  • 38
    • 0031762837 scopus 로고    scopus 로고
    • Measurement of the effectiveness of transitive sequence comparison, through a third 'intermediate' sequence
    • Gerstein,M. (1998) Measurement of the effectiveness of transitive sequence comparison, through a third 'intermediate' sequence. Bioinformatics, 14, 707-714.
    • (1998) Bioinformatics , vol.14 , pp. 707-714
    • Gerstein, M.1
  • 39
    • 0034237578 scopus 로고    scopus 로고
    • Large-scale comparison of protein sequence alignment algorithms with structure alignments
    • Sauder,J.M., Arthur,J.W. and Dunbrack,R.L.,Jr (2000) Large-scale comparison of protein sequence alignment algorithms with structure alignments. Proteins Struct. Funct. Genet., 40, 6-22.
    • (2000) Proteins Struct. Funct. Genet. , vol.40 , pp. 6-22
    • Sauder, J.M.1    Arthur, J.W.2    Dunbrack R.L., Jr.3
  • 40
    • 0033574503 scopus 로고    scopus 로고
    • Gleaning non-trivial structural, functional and evolutionary information about proteins by iterative database searches
    • Aravind,L. and Koonin,E.V. (1999) Gleaning non-trivial structural, functional and evolutionary information about proteins by iterative database searches. J. Mol. Biol., 287, 1023-1040.
    • (1999) J. Mol. Biol. , vol.287 , pp. 1023-1040
    • Aravind, L.1    Koonin, E.V.2
  • 41
    • 0036145804 scopus 로고    scopus 로고
    • A comparison of position-specific score matrices based on sequence and structure alignments
    • Panchenko,A. and Bryant,S. (2002) A comparison of position-specific score matrices based on sequence and structure alignments. Protein Sci., 11, 361-370.
    • (2002) Protein Sci. , vol.11 , pp. 361-370
    • Panchenko, A.1    Bryant, S.2
  • 42
    • 0033168097 scopus 로고    scopus 로고
    • A comprehensive comparison of multiple sequence alignment programs
    • Thompson,J.D., Plewniak,F. and Poch,O. (1999) A comprehensive comparison of multiple sequence alignment programs. Nucleic Acids Res., 27, 2682-2690.
    • (1999) Nucleic Acids Res. , vol.27 , pp. 2682-2690
    • Thompson, J.D.1    Plewniak, F.2    Poch, O.3
  • 44
    • 0016990971 scopus 로고
    • The origin and evolution of protein superfamilies
    • Dayhoff,M.O. (1976) The origin and evolution of protein superfamilies. Fed. Proc., 35, 2132-2138.
    • (1976) Fed. Proc. , vol.35 , pp. 2132-2138
    • Dayhoff, M.O.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.