메뉴 건너뛰기




Volumn 32, Issue 9, 2004, Pages 2838-2843

Frequency of gaps observed in a structurally aligned protein pair database suggests a simple gap penalty function

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONTROLLED STUDY; GENETIC ALGORITHM; LINEAR REGRESSION ANALYSIS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN MODIFICATION; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; BIOLOGY; EVALUATION; METHODOLOGY; PROBABILITY; PROTEIN TERTIARY STRUCTURE;

EID: 3042852894     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkh610     Document Type: Article
Times cited : (18)

References (27)
  • 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
    • 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
  • 4
    • 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
  • 5
    • 0037440190 scopus 로고    scopus 로고
    • Finding weak similarities between proteins by sequence profile comparison
    • Panchenko,A.R. (2003) Finding weak similarities between proteins by sequence profile comparison. Nucleic Acids Res., 31, 683-689.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 683-689
    • Panchenko, A.R.1
  • 6
    • 0025259313 scopus 로고
    • Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes
    • Karlin,S. and Altschul,S.F. (1990) Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc. Natl Acad. Sci. USA, 87, 2264-2268.
    • (1990) Proc. Natl. Acad. Sci. USA , vol.87 , pp. 2264-2268
    • Karlin, S.1    Altschul, S.F.2
  • 7
    • 0032126517 scopus 로고    scopus 로고
    • Generalized affine gap costs for protein sequence alignment
    • Altschul,S.F. (1998) Generalized affine gap costs for protein sequence alignment. Proteins, 32, 88-96.
    • (1998) Proteins , vol.32 , pp. 88-96
    • Altschul, S.F.1
  • 8
    • 0032770364 scopus 로고    scopus 로고
    • Local sequence alignments with monotonic gap penalties
    • Mott,R. (1999) Local sequence alignments with monotonic gap penalties. Bioinformatics, 15, 455-462.
    • (1999) Bioinformatics , vol.15 , pp. 455-462
    • Mott, R.1
  • 9
    • 0036854402 scopus 로고    scopus 로고
    • Empirical determination of effective gap penalties for sequence comparison
    • Reese,J.T. and Pearson,W.R. (2002) Empirical determination of effective gap penalties for sequence comparison. Bioinformatics, 18, 1500-1507.
    • (2002) Bioinformatics , vol.18 , pp. 1500-1507
    • Reese, J.T.1    Pearson, W.R.2
  • 10
    • 0024985346 scopus 로고
    • Optimal sequence alignment allowing for long gaps
    • Gotoh,O. (1990) Optimal sequence alignment allowing for long gaps Bull. Math. Biol., 52, 359-373.
    • (1990) Bull. Math. Biol. , vol.52 , pp. 359-373
    • Gotoh, O.1
  • 11
    • 0027483434 scopus 로고
    • Empirical and structural models for insertions and deletions in divergent evolution of proteins
    • Benner,S.A., Cohen,M. and Gonnet,G.H. (1993) Empirical and structural models for insertions and deletions in divergent evolution of proteins. J. Mol. Biol., 229, 1065-1082.
    • (1993) J. Mol. Biol. , vol.229 , pp. 1065-1082
    • Benner, S.A.1    Cohen, M.2    Gonnet, G.H.3
  • 12
    • 0028943946 scopus 로고
    • The size distribution of insertions and deletions in human and rodent pseudogenes suggests the logarithmic gap penalty for sequence alignment
    • Gu,X. and Li,W.H. (1995) The size distribution of insertions and deletions in human and rodent pseudogenes suggests the logarithmic gap penalty for sequence alignment. J. Mol. Evol., 40, 464-473.
    • (1995) J. Mol. Evol. , vol.40 , pp. 464-473
    • Gu, X.1    Li, W.H.2
  • 13
    • 0035479653 scopus 로고    scopus 로고
    • Distribution of indel lengths
    • Qian,B. and Goldstein,R.A. (2001) Distribution of indel lengths. Proteins, 45, 102-104.
    • (2001) Proteins , vol.45 , pp. 102-104
    • Qian, B.1    Goldstein, R.A.2
  • 14
    • 0029785147 scopus 로고    scopus 로고
    • Mapping the protein universe
    • Holm,L. and Sander,C. (1996) Mapping the protein universe. Science, 273, 595-603.
    • (1996) Science , vol.273 , pp. 595-603
    • Holm, L.1    Sander, C.2
  • 15
    • 0345306317 scopus 로고    scopus 로고
    • Patterns of nucleotide substitution, insertion and deletion in the human genome inferred from pseudogenes
    • Zhang,Z. and Gerstein,M. (2003) Patterns of nucleotide substitution, insertion and deletion in the human genome inferred from pseudogenes. Nucleic Acids Res., 31, 5338-5348.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 5338-5348
    • Zhang, Z.1    Gerstein, M.2
  • 16
    • 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
  • 17
    • 0033977581 scopus 로고    scopus 로고
    • The ASTRAL compendium for protein structure and sequence analysis
    • Brenner,S.E., Koehl,P. and Levitt,M. (2000) The ASTRAL compendium for protein structure and sequence analysis. Nucleic Acids Res., 28, 254-256.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 254-256
    • Brenner, S.E.1    Koehl, P.2    Levitt, M.3
  • 18
    • 0033833116 scopus 로고    scopus 로고
    • Protein structure alignment using environmental profiles
    • Jung,J. and Lee,B. (2000) Protein structure alignment using environmental profiles. Protein Eng., 13, 535-543.
    • (2000) Protein Eng. , vol.13 , pp. 535-543
    • Jung, J.1    Lee, B.2
  • 19
    • 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
  • 20
    • 0037058927 scopus 로고    scopus 로고
    • The directional atomic solvation energy: An atom-based potential for the assignment of protein sequences to known folds
    • Mallick,P., Weiss,R. and Eisenberg,D. (2002) The directional atomic solvation energy: an atom-based potential for the assignment of protein sequences to known folds. Proc. Natl Acad. Sci. USA, 99, 16041-16046.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 16041-16046
    • Mallick, P.1    Weiss, R.2    Eisenberg, D.3
  • 22
    • 0025317502 scopus 로고
    • Definition of general topological equivalence in protein structures. A procedure involving comparison of properties and relationships through simulated annealing and dynamic programming
    • Sali,A. and Blundell,T.L. (1990) Definition of general topological equivalence in protein structures. A procedure involving comparison of properties and relationships through simulated annealing and dynamic programming. J. Mol. Biol., 212, 403-428.
    • (1990) J. Mol. Biol. , vol.212 , pp. 403-428
    • Sali, A.1    Blundell, T.L.2
  • 23
    • 0023256559 scopus 로고
    • Slipped-strand mispairing: A major mechanism for DNA sequence evolution
    • Levinson,G. and Gutman,G.A. (1987) Slipped-strand mispairing: a major mechanism for DNA sequence evolution. Mol. Biol. Evol., 4, 203-221.
    • (1987) Mol. Biol. Evol. , vol.4 , pp. 203-221
    • Levinson, G.1    Gutman, G.A.2
  • 24
    • 0037370461 scopus 로고    scopus 로고
    • Evolution of alternative splicing: Deletions, insertions and origin of functional parts of proteins from intron sequences
    • Kondrashov,F.A. and Koonin,E.V. (2003) Evolution of alternative splicing: deletions, insertions and origin of functional parts of proteins from intron sequences. Trends Genet., 19, 115-119.
    • (2003) Trends Genet. , vol.19 , pp. 115-119
    • Kondrashov, F.A.1    Koonin, E.V.2
  • 25
    • 0024236865 scopus 로고
    • Sequence comparisons with concave weighting functions
    • Miller,W. and Myers,E.W. (1988) Sequence comparisons with concave weighting functions. Bull. Math. Biol., 50, 97-120.
    • (1988) Bull. Math. Biol. , vol.50 , pp. 97-120
    • Miller, W.1    Myers, E.W.2
  • 26
    • 0035967880 scopus 로고    scopus 로고
    • FUGUE: Sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties
    • Shi,J., Blundell,T.L. and Mizuguchi,K. (2001) FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. J. Mol. Biol., 310, 243-257.
    • (2001) J. Mol. Biol. , vol.310 , pp. 243-257
    • Shi, J.1    Blundell, T.L.2    Mizuguchi, K.3
  • 27
    • 0001642687 scopus 로고
    • Some biological sequence metrics
    • Waterman,M.S. and Beyer,W.A. (1976) Some biological sequence metrics. Adv. Math., 20, 367-387.
    • (1976) Adv. Math. , vol.20 , pp. 367-387
    • Waterman, M.S.1    Beyer, W.A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.