메뉴 건너뛰기




Volumn 21, Issue 19, 2005, Pages 3704-3710

Pairwise alignment incorporating dipeptide covariation

Author keywords

[No Author keywords available]

Indexed keywords

DIPEPTIDE;

EID: 27544499548     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bti616     Document Type: Article
Times cited : (16)

References (46)
  • 1
    • 0025878149 scopus 로고
    • Amino acid substitution matrices from an information theoretic perspective
    • Altschul,S.F. (1991) Amino acid substitution matrices from an information theoretic perspective. J. Mol. Biol., 219, 555-565.
    • (1991) J. Mol. Biol. , vol.219 , pp. 555-565
    • Altschul, S.F.1
  • 2
    • 0027516090 scopus 로고
    • A protein alignment scoring system sensitive at all evolutionary distances
    • Altschul,S.F. (1993) A protein alignment scoring system sensitive at all evolutionary distances. J. Mol. Evol., 36, 290-300.
    • (1993) J. Mol. Evol. , vol.36 , pp. 290-300
    • Altschul, S.F.1
  • 3
    • 0022899010 scopus 로고
    • Optimal sequence alignment using affine gap costs
    • Altschul,S.F. and Erickson,B.W. (1986) Optimal sequence alignment using affine gap costs. Bull. Math. Biol., 48, 603-616.
    • (1986) Bull. Math. Biol. , vol.48 , pp. 603-616
    • Altschul, S.F.1    Erickson, B.W.2
  • 4
    • 0025183708 scopus 로고
    • Basic local alignment search tool
    • Altschul,S.F. et al. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
    • (1990) J. Mol. Biol. , vol.215 , pp. 403-410
    • Altschul, S.F.1
  • 5
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
    • Altschul,S.F. 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.F.1
  • 6
    • 0035991777 scopus 로고    scopus 로고
    • Estimating and evaluating the statistics of gapped local-alignment scores
    • Bailey,T.L. and Gribskov,M. (2002) Estimating and evaluating the statistics of gapped local-alignment scores. J. Comput. Biol., 9, 575-593.
    • (2002) J. Comput. Biol. , vol.9 , pp. 575-593
    • Bailey, T.L.1    Gribskov, M.2
  • 7
    • 0022474446 scopus 로고
    • Maximum likelihood alignment of DNA sequences
    • Bishop,M.J. and Thompson,E.A. (1986) Maximum likelihood alignment of DNA sequences. J. Mol. Biol, 190, 159-165.
    • (1986) J. Mol. Biol , vol.190 , pp. 159-165
    • Bishop, M.J.1    Thompson, E.A.2
  • 8
    • 0013675412 scopus 로고    scopus 로고
    • Molecular propinquity: Evolutionary and structural relationships of proteins
    • PhD thesis, Cambridge University
    • Brenner,S.E. (1996). Molecular propinquity: Evolutionary and structural relationships of proteins. PhD thesis, Cambridge University.
    • (1996)
    • Brenner, S.E.1
  • 9
    • 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
  • 10
    • 0348129526 scopus 로고    scopus 로고
    • The ASTRAL Compendium in 2004
    • Chandonia,J.-M. et al. (2004) The ASTRAL Compendium in 2004. Nucleic Acids Res., 32, 189-192.
    • (2004) Nucleic Acids Res. , vol.32 , pp. 189-192
    • Chandonia, J.-M.1
  • 11
    • 0036780779 scopus 로고    scopus 로고
    • Information-theoretic dissection of pairwise contact potentials
    • Cline,M.S. et al. (2002) Information-theoretic dissection of pairwise contact potentials. Proteins, 49, 7-14.
    • (2002) Proteins , vol.49 , pp. 7-14
    • Cline, M.S.1
  • 13
    • 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, 1603-1611.
    • (2004) Bioinformatics , vol.20 , pp. 1603-1611
    • Crooks, G.E.1    Brenner, S.E.2
  • 14
    • 16344374083 scopus 로고    scopus 로고
    • An alternative model of amino acid replacement
    • Crooks,G.E. and Brenner,S.E. (2005) An alternative model of amino acid replacement. Bioinformatics, 21, 975-980.
    • (2005) Bioinformatics , vol.21 , pp. 975-980
    • Crooks, G.E.1    Brenner, S.E.2
  • 15
    • 10344246563 scopus 로고    scopus 로고
    • Measurements of protein sequence-structure correlations
    • Crooks,G.E. et al. (2004) Measurements of protein sequence-structure correlations. Proteins, 57, 804-810.
    • (2004) Proteins , vol.57 , pp. 804-810
    • Crooks, G.E.1
  • 16
    • 0000228203 scopus 로고
    • A model of evolutionary change in proteins
    • Dayhoff,M.O. et al. (1978) A model of evolutionary change in proteins. Atlas of Protein Sequences and Structure, 5(Suppl 3), 345-352.
    • (1978) Atlas of Protein Sequences and Structure , vol.5 , Issue.SUPPL. 3 , pp. 345-352
    • Dayhoff, M.O.1
  • 17
    • 0026817136 scopus 로고
    • Reconstructing history with amino acid sequences
    • Doolittle,R.F. (1992) Reconstructing history with amino acid sequences. Protein Sci., 1, 191-200.
    • (1992) Protein Sci. , vol.1 , pp. 191-200
    • Doolittle, R.F.1
  • 20
    • 0002344794 scopus 로고
    • Bootstrap methods: Another look at the jacknife
    • Efron,B. (1979) Bootstrap methods: Another look at the jacknife. Ann. Stat., 7, 1-26.
    • (1979) Ann. Stat. , vol.7 , pp. 1-26
    • Efron, B.1
  • 21
    • 0036301488 scopus 로고    scopus 로고
    • Detecting compensatory covariation signals in protein evolution using reconstructed ancestral sequences
    • Fukami-Kobayashi,K. et al. (2002) Detecting compensatory covariation signals in protein evolution using reconstructed ancestral sequences. J. Mol. Biol., 319, 729-743.
    • (2002) J. Mol. Biol. , vol.319 , pp. 729-743
    • Fukami-Kobayashi, K.1
  • 22
    • 0031805465 scopus 로고    scopus 로고
    • Assessing the impact of secondary structure and solvent accessibility on protein evolution
    • Goldman,N. et al. (1998) Assessing the impact of secondary structure and solvent accessibility on protein evolution. Genetics, 149, 445-458.
    • (1998) Genetics , vol.149 , pp. 445-458
    • Goldman, N.1
  • 23
    • 0028279408 scopus 로고
    • Analysis of amino-acid substitution during divergent evolution - The 400 by 400 dipeptide substitution matrix
    • Gonnet,G.H. et al. (1994) Analysis of amino-acid substitution during divergent evolution - the 400 by 400 dipeptide substitution matrix. Biochem. Biophys. Res. Comm., 199, 489-496.
    • (1994) Biochem. Biophys. Res. Comm. , vol.199 , pp. 489-496
    • Gonnet, G.H.1
  • 24
    • 0345983651 scopus 로고    scopus 로고
    • Bootstrapping and normalization for enhanced evaluations of pairwise sequence comparison
    • Green,R.E. and Brenner,S.E. (2002) Bootstrapping and normalization for enhanced evaluations of pairwise sequence comparison. Proc. IEEE, 90, 1834-1847.
    • (2002) Proc. IEEE , vol.90 , pp. 1834-1847
    • Green, R.E.1    Brenner, S.E.2
  • 25
    • 0033977579 scopus 로고    scopus 로고
    • Increased coverage of protein families with the blocks database servers
    • Henikoff,J.G. et al. (2000) Increased coverage of protein families with the blocks database servers. Nucleic Acids Res., 28, 228-230.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 228-230
    • Henikoff, J.G.1
  • 26
    • 0026458378 scopus 로고
    • Amino-acid substitution matrices from protein blocks
    • Henikoff,S. and Henikoff,J.G. (1992) Amino-acid substitution matrices from protein blocks. Proc. Natl Acad. Sci. USA, 89, 10915-10919.
    • (1992) Proc. Natl. Acad. Sci. USA , vol.89 , pp. 10915-10919
    • Henikoff, S.1    Henikoff, J.G.2
  • 27
    • 0033842326 scopus 로고    scopus 로고
    • Use of residue pairs in protein sequence-sequence and sequence-structure alignments
    • Jung,J.S. and Lee,B. (2000) Use of residue pairs in protein sequence-sequence and sequence-structure alignments. Protein Sci., 9, 1576-1588.
    • (2000) Protein Sci. , vol.9 , pp. 1576-1588
    • Jung, J.S.1    Lee, B.2
  • 28
    • 0032438987 scopus 로고    scopus 로고
    • Hidden Markov models for detecting remote protein homologies
    • Karplus,K. et al. (1998) Hidden Markov models for detecting remote protein homologies. Bioinformatics, 14, 846-856.
    • (1998) Bioinformatics , vol.14 , pp. 846-856
    • Karplus, K.1
  • 29
    • 0038010382 scopus 로고    scopus 로고
    • Testing homology with Contact Accepted mutatiOn (CAO)
    • Lin,K. et al. (2003) Testing homology with Contact Accepted mutatiOn (CAO). Comput. Biol. Chem., 27, 93-102.
    • (2003) Comput. Biol. Chem. , vol.27 , pp. 93-102
    • Lin, K.1
  • 30
    • 0036134748 scopus 로고    scopus 로고
    • Estimating amino acid substitution models: A comparison of Dayhoff's estimator, the resolvent approach and a maximum likelihood method
    • Müller,T. et al. (2002) Estimating amino acid substitution models: A comparison of Dayhoff's estimator, the resolvent approach and a maximum likelihood method. Mol. Biol. Evol., 19, 8-13.
    • (2002) Mol. Biol. Evol. , vol.19 , pp. 8-13
    • Müller, T.1
  • 31
    • 0028961335 scopus 로고
    • SCOP: A structural classification of proteins database for the investigation of sequences and structures
    • Murzin,A.G. et al. (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
  • 32
    • 0032509105 scopus 로고    scopus 로고
    • Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods
    • Park,J. et al. (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
  • 33
    • 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
  • 34
    • 27544471726 scopus 로고    scopus 로고
    • Statistical evaluation of pairwise protein sequence comparison with the Bayesian bootstrap
    • doi:10.1093/bioinformatics/bti627
    • Price,G.A. et al. (2005) Statistical evaluation of pairwise protein sequence comparison with the Bayesian bootstrap. Bioinformatics, doi:10.1093/bioinformatics/bti627
    • (2005) Bioinformatics
    • Price, G.A.1
  • 35
    • 0028557303 scopus 로고
    • Residue-residue contact substitution probabilities derived from aligned three-dimensional structures and the identification of common folds
    • Rodionov,M.A. and Johnson,M.S. (1994) Residue-residue contact substitution probabilities derived from aligned three-dimensional structures and the identification of common folds. Protein Sci., 3, 2366-2377.
    • (1994) Protein. Sci. , vol.3 , pp. 2366-2377
    • Rodionov, M.A.1    Johnson, M.S.2
  • 36
    • 0000135972 scopus 로고
    • The Bayesian bootstrap
    • Rubin,D.B. (1981) The Bayesian bootstrap. Ann. Stat., 9, 130-134.
    • (1981) Ann. Stat. , vol.9 , pp. 130-134
    • Rubin, D.B.1
  • 37
    • 0026030641 scopus 로고
    • Database of homology-derived protein structures and the structural meaning of sequence alignment
    • Sander,C. and Schneider,R. (1991) Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins, 9, 56-68.
    • (1991) Proteins , vol.9 , pp. 56-68
    • Sander, C.1    Schneider, R.2
  • 38
    • 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
  • 39
    • 0029985399 scopus 로고    scopus 로고
    • Combining protein evolution and secondary structure
    • Thorne,J.L. et al. (1996) Combining protein evolution and secondary structure. Mol. Biol. Evol., 13, 666-673.
    • (1996) Mol. Biol. Evol. , vol.13 , pp. 666-673
    • Thorne, J.L.1
  • 40
    • 0026079507 scopus 로고
    • An evolutionary model for maximum likelihood alignment of DNA sequences
    • Thorne,J.L. et al. (1991) An evolutionary model for maximum likelihood alignment of DNA sequences. J. Mol. Evol., 33, 114-124.
    • (1991) J. Mol. Evol. , vol.33 , pp. 114-124
    • Thorne, J.L.1
  • 41
    • 0026528734 scopus 로고
    • Inching toward reality: An improved likelihood model of sequence evolution
    • Thorne,J.L. et al. (1992) Inching toward reality: An improved likelihood model of sequence evolution. J. Mol. Evol., 34, 3-16.
    • (1992) J. Mol. Evol. , vol.34 , pp. 3-16
    • Thorne, J.L.1
  • 42
    • 0031023842 scopus 로고    scopus 로고
    • Prediction of the stability of protein mutants based on structural environment-dependent amino acid substitution and propensity tables
    • Topham,C.M. et al. (1997) Prediction of the stability of protein mutants based on structural environment-dependent amino acid substitution and propensity tables. Protein Eng., 10, 7-21.
    • (1997) Protein Eng. , vol.10 , pp. 7-21
    • Topham, C.M.1
  • 43
    • 0034619248 scopus 로고    scopus 로고
    • Information content of protein sequences
    • Weiss,O. et al. (2000) Information content of protein sequences. J. Theor. Biol., 206, 379-386.
    • (2000) J. Theor. Biol. , vol.206 , pp. 379-386
    • Weiss, O.1
  • 44
    • 0346734129 scopus 로고    scopus 로고
    • The compositional adjustment of amino acid substitution matrices
    • Yu,Y.K. et al. (2003) The compositional adjustment of amino acid substitution matrices. Proc. Natl Acad. Sci. USA, 100, 15688-15693.
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 15688-15693
    • Yu, Y.K.1
  • 46
    • 11344287710 scopus 로고    scopus 로고
    • A generalized affine gap model significantly improves protein sequence alignment accuracy
    • Zachariah,M.A. et al. (2005) A generalized affine gap model significantly improves protein sequence alignment accuracy. Proteins, 58, 329-338.
    • (2005) Proteins , vol.58 , pp. 329-338
    • Zachariah, M.A.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.