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Volumn 3, Issue , 2002, Pages

Identification and characterization of subfamily-specific signatures in a large protein superfamily by a hidden Markov model approach

Author keywords

[No Author keywords available]

Indexed keywords

CADHERIN; CALCIUM ION; HELIX LOOP HELIX PROTEIN; CALCIUM BINDING PROTEIN; PARVALBUMIN; PROTEIN; PROTEOME;

EID: 0012035566     PISSN: 14712105     EISSN: None     Source Type: Journal    
DOI: 10.1186/1471-2105-3-1     Document Type: Article
Times cited : (12)

References (40)
  • 2
    • 0028309899 scopus 로고
    • Using the FASTA program to search protein and DNA sequence databases
    • Pearson WR: Using the FASTA program to search protein and DNA sequence databases. Methods Mol Biol 1994, 25:365-389
    • (1994) Methods Mol. Biol. , vol.25 , pp. 365-389
    • Pearson, W.R.1
  • 4
    • 0032776495 scopus 로고    scopus 로고
    • Blocks+: A non-redundant database of protein alignment blocks derived from multiple compilations
    • Henikoff S, Henikoff JG, Pietrokovski S: Blocks+: a non-redundant database of protein alignment blocks derived from multiple compilations. Bioinformatics 1999, 15:471-479
    • (1999) Bioinformatics , vol.15 , pp. 471-479
    • Henikoff, S.1    Henikoff, J.G.2    Pietrokovski, S.3
  • 5
    • 0025303764 scopus 로고
    • Protein multiple sequence alignment and flexible pattern matching
    • Barton GJ: Protein multiple sequence alignment and flexible pattern matching. Methods Enzymol 1990, 183:403-428
    • (1990) Methods Enzymol. , vol.183 , pp. 403-428
    • Barton, G.J.1
  • 6
    • 0031743421 scopus 로고    scopus 로고
    • Profile hidden Markov models
    • Eddy SR: Profile hidden Markov models. Bioinformatics 1998, 14:755-763
    • (1998) Bioinformatics , vol.14 , pp. 755-763
    • Eddy, S.R.1
  • 8
    • 0032568655 scopus 로고    scopus 로고
    • SMART, a simple modular architecture research tool: Identification of signaling domains
    • Schultz J, Milpetz F, Bork P, Ponting CP: SMART, a simple modular architecture research tool: identification of signaling domains. Proc Natl Acad Sci USA 1998, 95:5857-5864
    • (1998) Proc. Natl. Acad. Sci. USA , vol.95 , pp. 5857-5864
    • Schultz, J.1    Milpetz, F.2    Bork, P.3    Ponting, C.P.4
  • 12
    • 0033957841 scopus 로고    scopus 로고
    • ProDom and ProDom-CG: Tools for protein domain analysis and whole genome comparisons
    • Corpet F, Servant F, Gouzy J, Kahn D: ProDom and ProDom-CG: tools for protein domain analysis and whole genome comparisons. Nucleic Acids Res 2000, 28:267-269
    • (2000) Nucleic Acids Res. , vol.28 , pp. 267-269
    • Corpet, F.1    Servant, F.2    Gouzy, J.3    Kahn, D.4
  • 16
    • 0032454584 scopus 로고    scopus 로고
    • Classification and evolution of EF-hand proteins
    • Kawasaki H, Nakayama S, Kretsinger RH: Classification and evolution of EF-hand proteins. Biometals 1998, 11:277-295
    • (1998) Biometals , vol.11 , pp. 277-295
    • Kawasaki, H.1    Nakayama, S.2    Kretsinger, R.H.3
  • 17
    • 0016990971 scopus 로고
    • The origin and evolution of protein superfamilies
    • Dayhoff MO: The origin and evolution of protein superfamilies. Fed Proc 1976, 35:2132-2138
    • (1976) Fed. Proc. , vol.35 , pp. 2132-2138
    • Dayhoff, M.O.1
  • 18
    • 0029913807 scopus 로고    scopus 로고
    • An evolutionary trace method defines binding surfaces common to protein families
    • Lichtarge O, Bourne HR, Cohen FE: An evolutionary trace method defines binding surfaces common to protein families. J Mol Biol 1996, 257:342-358
    • (1996) J. Mol. Biol. , vol.257 , pp. 342-358
    • Lichtarge, O.1    Bourne, H.R.2    Cohen, F.E.3
  • 19
    • 0033493228 scopus 로고    scopus 로고
    • Browsing protein families via the 'Rich Family Description' format
    • Corpet F, Gouzy J, Kahn D: Browsing protein families via the 'Rich Family Description' format. Bioinformatics 1999, 15:1020-1027
    • (1999) Bioinformatics , vol.15 , pp. 1020-1027
    • Corpet, F.1    Gouzy, J.2    Kahn, D.3
  • 20
    • 0031604140 scopus 로고    scopus 로고
    • Phylogenetic inference in protein superfamilies: Analysis of SH2 domains
    • Sjolander K: Phylogenetic inference in protein superfamilies: analysis of SH2 domains. Proc Int Conf lntell Syst Mol Biol 1998, 6:165-174
    • (1998) Proc. Int. Conf. Intell. Syst. Mol. Biol. , vol.6 , pp. 165-174
    • Sjolander, K.1
  • 21
    • 0034897827 scopus 로고    scopus 로고
    • Secator: A program for inferring protein subfamilies from phylogenetic trees
    • Wicker N, Perrin GR, Thierry JC, Poch O: Secator: a program for inferring protein subfamilies from phylogenetic trees. Mol Biol Evol 2001, 18:1435-1441
    • (2001) Mol. Biol. Evol. , vol.18 , pp. 1435-1441
    • Wicker, N.1    Perrin, G.R.2    Thierry, J.C.3    Poch, O.4
  • 22
    • 0014757386 scopus 로고
    • A general method applicable to the search for similarities in the amino acid sequence of two proteins
    • Needleman SB, Wunsch CD: A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 1970, 48:443-453
    • (1970) J. Mol. Biol. , vol.48 , pp. 443-453
    • Needleman, S.B.1    Wunsch, C.D.2
  • 23
    • 0028092214 scopus 로고
    • Amino acid substitution during functionally constrained divergent evolution of protein sequences
    • Benner SA, Cohen MA, Gonnet GH: Amino acid substitution during functionally constrained divergent evolution of protein sequences. Protein Eng 1994, 7:1323-1332
    • (1994) Protein Eng. , vol.7 , pp. 1323-1332
    • Benner, S.A.1    Cohen, M.A.2    Gonnet, G.H.3
  • 24
    • 0017885731 scopus 로고
    • A comprehensive examination of protein sequences for evidence of internal gene duplication
    • Barker WC, Ketcham LK, Dayhoff MO: A comprehensive examination of protein sequences for evidence of internal gene duplication. J Mol Evol 1978, 10:265-281
    • (1978) J. Mol. Evol. , vol.10 , pp. 265-281
    • Barker, W.C.1    Ketcham, L.K.2    Dayhoff, M.O.3
  • 25
    • 0017855376 scopus 로고
    • Construction of phylogenetic trees for proteins and nucleic acids: Empirical evaluation of alternative matrix methods
    • Prager EM, Wilson AC: Construction of phylogenetic trees for proteins and nucleic acids: empirical evaluation of alternative matrix methods. J Mol Evol 1978, 11:129-142
    • (1978) J. Mol. Evol. , vol.11 , pp. 129-142
    • Prager, E.M.1    Wilson, A.C.2
  • 26
    • 0034567210 scopus 로고    scopus 로고
    • Comparative protein structure modeling. Introduction and practical examples with modeller
    • Sanchez R, Sali A: Comparative protein structure modeling. Introduction and practical examples with modeller. Methods Mol Biol 2000, 143:97-129
    • (2000) Methods Mol. Biol. , vol.143 , pp. 97-129
    • Sanchez, R.1    Sali, A.2
  • 28
    • 0004267425 scopus 로고
    • The HMMER Package
    • Eddy SR: The HMMER Package. 1995
    • (1995)
    • Eddy, S.R.1
  • 30
    • 0025612251 scopus 로고
    • 2+-binding site of uvomorulin abolish the adhesive function
    • 2+-binding site of uvomorulin abolish the adhesive function. Cell 1990, 63:1033-1038
    • (1990) Cell , vol.63 , pp. 1033-1038
    • Ozawa, M.1    Engel, J.2    Kemler, R.3
  • 31
    • 0032928812 scopus 로고    scopus 로고
    • Structural view of cadherin-mediated cell-cell adhesion
    • Alattia JR, Kurokawa H, Ikura M: Structural view of cadherin-mediated cell-cell adhesion. Cell Mol Life Sci 1999, 55:359-367
    • (1999) Cell Mol. Life Sci. , vol.55 , pp. 359-367
    • Alattia, J.R.1    Kurokawa, H.2    Ikura, M.3
  • 32
    • 0015919772 scopus 로고
    • 2+-binding protein. II. Structure determination and general description
    • 2+-binding protein. II. Structure determination and general description. J Biol Chem 1973, 248:3313-3326
    • (1973) J. Biol. Chem. , vol.248 , pp. 3313-3326
    • Kretsinger, R.H.1    Nockolds, C.E.2
  • 34
    • 0029670471 scopus 로고    scopus 로고
    • +-binding stoichiometry of calbindin D28k as assessed by spectroscopic analyses of synthetic peptide fragments
    • +-binding stoichiometry of calbindin D28k as assessed by spectroscopic analyses of synthetic peptide fragments. Biochemistry 1996,35:3662-3669
    • (1996) Biochemistry , vol.35 , pp. 3662-3669
    • Akerfeldt, K.S.1    Coyne, A.N.2    Wilk, R.R.3    Thulin, E.4    Linse, S.5
  • 37
    • 0027516760 scopus 로고
    • Force relaxation, labile heat and parvalbumin content of skeletal muscle fibres of Xenopus laevis
    • Lannergren J, Elzinga G, Stienen GJ: Force relaxation, labile heat and parvalbumin content of skeletal muscle fibres of Xenopus laevis. J Physiol 1993, 463:123-140
    • (1993) J. Physiol. , vol.463 , pp. 123-140
    • Lannergren, J.1    Elzinga, G.2    Stienen, G.J.3
  • 38
  • 39
    • 0024447798 scopus 로고
    • 2+) and Cd- substituted carp parvalbumin using X-ray crystallographic data at 1.6-Å resolution
    • 2+) and Cd- substituted carp parvalbumin using X-ray crystallographic data at 1.6-Å resolution. J Biol Chem 1989, 264:16620-16628
    • (1989) J. Biol. Chem. , vol.264 , pp. 16620-16628
    • Swain, A.L.1    Kretsinger, R.H.2    Amma, E.L.3
  • 40
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • Thompson JD, Higgins DG, Gibson TJ: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994, 22:4673-4680
    • (1994) Nucleic Acids Res. , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.