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Volumn 3, Issue 11, 2008, Pages

Detecting clusters of mutations

Author keywords

[No Author keywords available]

Indexed keywords

DNA; PROTEIN; SOLVENT;

EID: 56649123164     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0003765     Document Type: Article
Times cited : (11)

References (80)
  • 1
    • 0026428610 scopus 로고
    • Adaptive protein evolution at the Adh locus in Drosophila
    • McDonald JH, Kreitman M (1991) Adaptive protein evolution at the Adh locus in Drosophila. Nature 351: 652-654.
    • (1991) Nature , vol.351 , pp. 652-654
    • McDonald, J.H.1    Kreitman, M.2
  • 2
    • 0031972161 scopus 로고    scopus 로고
    • Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene
    • Nielsen R, Yang Z (1998) Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics 148: 929-936.
    • (1998) Genetics , vol.148 , pp. 929-936
    • Nielsen, R.1    Yang, Z.2
  • 3
    • 0032849322 scopus 로고    scopus 로고
    • A method for detecting positive selection at single amino acid sites
    • Suzuki Y, Gojobori T (1999) A method for detecting positive selection at single amino acid sites. Mol Biol Evol 16: 1315-1328.
    • (1999) Mol Biol Evol , vol.16 , pp. 1315-1328
    • Suzuki, Y.1    Gojobori, T.2
  • 4
    • 0034575442 scopus 로고    scopus 로고
    • Methods to detect selection in populations with applications to the human
    • Kreitman M (2000) Methods to detect selection in populations with applications to the human. Annual Rev Genomics Human Gen 1: 539-559.
    • (2000) Annual Rev Genomics Human Gen , vol.1 , pp. 539-559
    • Kreitman, M.1
  • 5
    • 0037186564 scopus 로고    scopus 로고
    • Adaptive protein evolution in Drosophila
    • Smith NGC, Eyre-Walker A (2002) Adaptive protein evolution in Drosophila. Nature 415: 1022-1024.
    • (2002) Nature , vol.415 , pp. 1022-1024
    • Smith, N.G.C.1    Eyre-Walker, A.2
  • 6
    • 0037167852 scopus 로고    scopus 로고
    • Detecting recent positive selection in the human genome from haplotype structure
    • Sabeti PC, Reich DE, Higgins JM, Levine HZP, Richter DJ, et al. (2002) Detecting recent positive selection in the human genome from haplotype structure. Nature 419: 832-837.
    • (2002) Nature , vol.419 , pp. 832-837
    • Sabeti, P.C.1    Reich, D.E.2    Higgins, J.M.3    Levine, H.Z.P.4    Richter, D.J.5
  • 7
    • 8444220853 scopus 로고    scopus 로고
    • Three-dimensional window analysis for detecting positive selection at structural regions of proteins
    • Suzuki Y (2004) Three-dimensional window analysis for detecting positive selection at structural regions of proteins. Mol Biol Evol 21: 2352-2359.
    • (2004) Mol Biol Evol , vol.21 , pp. 2352-2359
    • Suzuki, Y.1
  • 9
    • 16344378246 scopus 로고    scopus 로고
    • Bayes empirical bayes inference of amino acid sites under positive selection
    • Yang Z, Wong WSW, Nielsen R (2005) Bayes empirical bayes inference of amino acid sites under positive selection. Mol Biol Evol 22: 1107-1118.
    • (2005) Mol Biol Evol , vol.22 , pp. 1107-1118
    • Yang, Z.1    Wong, W.S.W.2    Nielsen, R.3
  • 10
    • 34548431288 scopus 로고    scopus 로고
    • Rapid detection of positive selection in genes and genomes through variation clusters
    • Wagner A (2007) Rapid detection of positive selection in genes and genomes through variation clusters. Genetics 176: 2451-2463.
    • (2007) Genetics , vol.176 , pp. 2451-2463
    • Wagner, A.1
  • 11
    • 0019824131 scopus 로고
    • Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: A proposal for a synonymous codon choice that is optimal for the E. coli translational system
    • Ikemura T (1981) Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: a proposal for a synonymous codon choice that is optimal for the E. coli translational system. J Mol Biol 151: 389-409.
    • (1981) J Mol Biol , vol.151 , pp. 389-409
    • Ikemura, T.1
  • 12
    • 0028220048 scopus 로고
    • Synonymous codon usage in Drosophila melanogaster: Natural selection and translational accuracy
    • Akashi H (1994) Synonymous codon usage in Drosophila melanogaster: Natural selection and translational accuracy. Genetics 136: 927-935.
    • (1994) Genetics , vol.136 , pp. 927-935
    • Akashi, H.1
  • 13
    • 0028359705 scopus 로고
    • Codon usage in Caenorhabditis elegans: Delineation of translational selection and mutational biases
    • Stenico M, Lloyd AT, Sharp PM (1994) Codon usage in Caenorhabditis elegans: delineation of translational selection and mutational biases. Nucl Acids Res 22: 2437-2446.
    • (1994) Nucl Acids Res , vol.22 , pp. 2437-2446
    • Stenico, M.1    Lloyd, A.T.2    Sharp, P.M.3
  • 14
    • 33846786904 scopus 로고    scopus 로고
    • Synonymous codon usage in Escherichia coli: Selection for translational accuracy
    • Stoletzki N, Eyre-Walker A (2007) Synonymous codon usage in Escherichia coli: Selection for translational accuracy. Mol Biol Evol 24: 374-381.
    • (2007) Mol Biol Evol , vol.24 , pp. 374-381
    • Stoletzki, N.1    Eyre-Walker, A.2
  • 15
    • 10344224528 scopus 로고    scopus 로고
    • Adjusting for selection on synonymous sites in estimates of evolutionary distance
    • Hirsh AE, Fraser HB, Wall DP (2005) Adjusting for selection on synonymous sites in estimates of evolutionary distance. Mol Biol Evol 22: 174-177.
    • (2005) Mol Biol Evol , vol.22 , pp. 174-177
    • Hirsh, A.E.1    Fraser, H.B.2    Wall, D.P.3
  • 16
    • 30744441602 scopus 로고    scopus 로고
    • A single determinant dominates the rate of yeast protein evolution
    • Drummond DA, Raval A, Wilke CO (2006) A single determinant dominates the rate of yeast protein evolution. Mol Biol Evol 23: 327-337.
    • (2006) Mol Biol Evol , vol.23 , pp. 327-337
    • Drummond, D.A.1    Raval, A.2    Wilke, C.O.3
  • 17
    • 47549097539 scopus 로고    scopus 로고
    • Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution
    • Drummond DA, Wilke CO (2008) Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution. Cell 134: 341-352.
    • (2008) Cell , vol.134 , pp. 341-352
    • Drummond, D.A.1    Wilke, C.O.2
  • 18
    • 30744432134 scopus 로고    scopus 로고
    • Evidence for selection on synonymous mutations affecting stability of mRNA secondary structure in mammals
    • Chamary JV, Hurst LD (2005) Evidence for selection on synonymous mutations affecting stability of mRNA secondary structure in mammals. Genome Biology 6: R75.
    • (2005) Genome Biology , vol.6
    • Chamary, J.V.1    Hurst, L.D.2
  • 19
    • 30744469841 scopus 로고    scopus 로고
    • Evidence for purifying selection against synonymous mutations in mammalian exonic splicing enhancers
    • Parmley JL, Chamary JV, Hurst LD (2006) Evidence for purifying selection against synonymous mutations in mammalian exonic splicing enhancers. Mol Biol Evol 23: 301-309.
    • (2006) Mol Biol Evol , vol.23 , pp. 301-309
    • Parmley, J.L.1    Chamary, J.V.2    Hurst, L.D.3
  • 20
    • 34748817463 scopus 로고    scopus 로고
    • Looking for Darwin in all the wrong places: The misguided quest for positive selection at the nucleotide sequence level
    • Hughes AL (2007) Looking for Darwin in all the wrong places: The misguided quest for positive selection at the nucleotide sequence level. Heredity 99: 364-373.
    • (2007) Heredity , vol.99 , pp. 364-373
    • Hughes, A.L.1
  • 21
    • 51649108111 scopus 로고    scopus 로고
    • The origin of adaptive phenotypes
    • Hughes AL (2008) The origin of adaptive phenotypes. Natl Acad Sci USA 105: 13193-13194.
    • (2008) Natl Acad Sci USA , vol.105 , pp. 13193-13194
    • Hughes, A.L.1
  • 22
    • 48149108739 scopus 로고    scopus 로고
    • Codon-based tests of positive selection, branch lengths, and the evolution of mammalian immune system genes
    • Hughes AL, Friedman R (2008) Codon-based tests of positive selection, branch lengths, and the evolution of mammalian immune system genes. Immunogenetics 60: 495-506.
    • (2008) Immunogenetics , vol.60 , pp. 495-506
    • Hughes, A.L.1    Friedman, R.2
  • 23
    • 51649122492 scopus 로고    scopus 로고
    • Elucidation of phenotypic adaptations: Molecular analyses of dim-light vision proteins in vertebrates
    • Yokoyama S, Tada T, Zhang H, Britt L (2008) Elucidation of phenotypic adaptations: Molecular analyses of dim-light vision proteins in vertebrates. Proc Natl Acad Sci USA 105: 13480-13485.
    • (2008) Proc Natl Acad Sci USA , vol.105 , pp. 13480-13485
    • Yokoyama, S.1    Tada, T.2    Zhang, H.3    Britt, L.4
  • 24
    • 0029980416 scopus 로고    scopus 로고
    • New statistical tests of neutrality for DNA samples from a population
    • Fu Y (1996) New statistical tests of neutrality for DNA samples from a population. Genetics 143: 557-570.
    • (1996) Genetics , vol.143 , pp. 557-570
    • Fu, Y.1
  • 25
    • 0024313579 scopus 로고
    • Statistical method for testing the neutral mutation hypothesis by DNA polymorphism
    • Tajima F (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.
    • (1989) Genetics , vol.123 , pp. 585-595
    • Tajima, F.1
  • 26
    • 0033870688 scopus 로고    scopus 로고
    • When did the human population size start increasing?
    • Wall JD, Przeworski M (2000) When did the human population size start increasing? Genetics 155: 1865-1874.
    • (2000) Genetics , vol.155 , pp. 1865-1874
    • Wall, J.D.1    Przeworski, M.2
  • 27
    • 0037307413 scopus 로고    scopus 로고
    • Signatures of natural selection in the human genome
    • Bamshad M, Wooding SP (2003) Signatures of natural selection in the human genome. Nature Rev Genet 4: 99-111.
    • (2003) Nature Rev Genet , vol.4 , pp. 99-111
    • Bamshad, M.1    Wooding, S.P.2
  • 28
    • 24744465216 scopus 로고    scopus 로고
    • Inferring the effects of demography and selection on Drosophila melanogaster populations from a chromosome-wide scan of DNA variation
    • Ometto L, Glinka S, De Lorenzo D, Stephan W (2005) Inferring the effects of demography and selection on Drosophila melanogaster populations from a chromosome-wide scan of DNA variation. Mol Biol Evol 22: 2119-2130.
    • (2005) Mol Biol Evol , vol.22 , pp. 2119-2130
    • Ometto, L.1    Glinka, S.2    De Lorenzo, D.3    Stephan, W.4
  • 29
    • 0028808763 scopus 로고
    • Context-dependent optimal substitution matrices
    • Koshi JM, Goldstein RA (1995) Context-dependent optimal substitution matrices. Protein Engineering 8: 641-645.
    • (1995) Protein Engineering , vol.8 , pp. 641-645
    • Koshi, J.M.1    Goldstein, R.A.2
  • 30
    • 0031805465 scopus 로고    scopus 로고
    • Assessing the impact of secondary structure and solvent accessibility on protein evolution
    • Goldman N, Thorne JL, Jones DT (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    Thorne, J.L.2    Jones, D.T.3
  • 31
    • 0345062357 scopus 로고    scopus 로고
    • Universally conserved positions in protein folds: Reading evolutionary signals about stability, folding kinetics and function
    • Mirny LA, Shakhnovich EI (1999) Universally conserved positions in protein folds: reading evolutionary signals about stability, folding kinetics and function. J Mol Biol 291: 177-196.
    • (1999) J Mol Biol , vol.291 , pp. 177-196
    • Mirny, L.A.1    Shakhnovich, E.I.2
  • 32
  • 33
    • 33748143748 scopus 로고    scopus 로고
    • Structural determinants of the rate of protein evolution in yeast
    • Bloom JD, Drummond DA, Arnold FH, Wilke CO (2006) Structural determinants of the rate of protein evolution in yeast. Mol Biol Evol 23: 1751-1761.
    • (2006) Mol Biol Evol , vol.23 , pp. 1751-1761
    • Bloom, J.D.1    Drummond, D.A.2    Arnold, F.H.3    Wilke, C.O.4
  • 34
    • 34547809931 scopus 로고    scopus 로고
    • Quantifying the impact of protein tertiary structure on molecular evolution
    • Choi SC, Hobolth A, Robinson DM, Kishino H, Thorne JL (2007) Quantifying the impact of protein tertiary structure on molecular evolution. Mol Biol Evol 24: 1769-1782.
    • (2007) Mol Biol Evol , vol.24 , pp. 1769-1782
    • Choi, S.C.1    Hobolth, A.2    Robinson, D.M.3    Kishino, H.4    Thorne, J.L.5
  • 35
    • 33845875196 scopus 로고    scopus 로고
    • Relating three-dimensional structures to protein networks provides evolutionary insights
    • Kim PM, Lu LJ, Gerstein MB (2006) Relating three-dimensional structures to protein networks provides evolutionary insights. Science 314: 1882-1883.
    • (2006) Science , vol.314 , pp. 1882-1883
    • Kim, P.M.1    Lu, L.J.2    Gerstein, M.B.3
  • 36
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: A practical and powerful approach to multiple testing
    • Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: A practical and powerful approach to multiple testing. J Royal Stat Soc B 57: 289-300.
    • (1995) J Royal Stat Soc B , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 37
    • 0025147562 scopus 로고
    • Positive Darwinian selection promotes charge profile diversity in the antigen-binding cleft of class I major-histocompatibility-complex molecules
    • Hughes AL, Ota T, Nei M (1990) Positive Darwinian selection promotes charge profile diversity in the antigen-binding cleft of class I major-histocompatibility-complex molecules. Mol Biol Evol 7: 515-524.
    • (1990) Mol Biol Evol , vol.7 , pp. 515-524
    • Hughes, A.L.1    Ota, T.2    Nei, M.3
  • 38
    • 0033921902 scopus 로고    scopus 로고
    • Rates of conservative and radical nonsynonymous nucleotide substitutions in mammalian nuclear genes
    • Zhang J (2000) Rates of conservative and radical nonsynonymous nucleotide substitutions in mammalian nuclear genes. J Mol Evol 50: 56-68.
    • (2000) J Mol Evol , vol.50 , pp. 56-68
    • Zhang, J.1
  • 39
    • 0035986857 scopus 로고    scopus 로고
    • Ratios of radical to conservative amino acid replacement are affected by mutational and compositional factors and may not be indicative of positive Darwinian selection
    • Dagan T, Talmor Y, Graur D (2002) Ratios of radical to conservative amino acid replacement are affected by mutational and compositional factors and may not be indicative of positive Darwinian selection. Mol Biol Evol 19: 1022-1025.
    • (2002) Mol Biol Evol , vol.19 , pp. 1022-1025
    • Dagan, T.1    Talmor, Y.2    Graur, D.3
  • 40
    • 0142075815 scopus 로고    scopus 로고
    • Are radical and conservative substitution rates useful statistics in molecular evolution?
    • Smith NGC (2003) Are radical and conservative substitution rates useful statistics in molecular evolution? J Mol Evol 57: 467-478.
    • (2003) J Mol Evol , vol.57 , pp. 467-478
    • Smith, N.G.C.1
  • 41
    • 34548203941 scopus 로고    scopus 로고
    • Radical amino acid change versus positive selection in the evolution of viral envelope proteins
    • Hanada K, Gojobori T, Li WH (2006) Radical amino acid change versus positive selection in the evolution of viral envelope proteins. Gene 385: 83-88.
    • (2006) Gene , vol.385 , pp. 83-88
    • Hanada, K.1    Gojobori, T.2    Li, W.H.3
  • 42
    • 0031766244 scopus 로고    scopus 로고
    • What amino acid properties affect protein evolution?
    • Xia X, Li WH (1998) What amino acid properties affect protein evolution? J Mol Evol 47: 557-564.
    • (1998) J Mol Evol , vol.47 , pp. 557-564
    • Xia, X.1    Li, W.H.2
  • 43
    • 0034982702 scopus 로고    scopus 로고
    • Estimating the influence of selection on the variable amino acid sites of the cytochrome b protein functional domains
    • McClellan DA, McCracken KG (2001) Estimating the influence of selection on the variable amino acid sites of the cytochrome b protein functional domains. Mol Biol Evol 18: 917-925.
    • (2001) Mol Biol Evol , vol.18 , pp. 917-925
    • McClellan, D.A.1    McCracken, K.G.2
  • 44
    • 0016197604 scopus 로고
    • Amino acid difference formula to help explain protein evolution
    • Grantham R (1974) Amino acid difference formula to help explain protein evolution. Science 185: 862-864.
    • (1974) Science , vol.185 , pp. 862-864
    • Grantham, R.1
  • 45
    • 0020475449 scopus 로고
    • A simple method for displaying the hydropathic character of a protein
    • Kyte J, Doolittle RF (1982) A simple method for displaying the hydropathic character of a protein. J Mol Biol 157: 105-132.
    • (1982) J Mol Biol , vol.157 , pp. 105-132
    • Kyte, J.1    Doolittle, R.F.2
  • 46
    • 0014349825 scopus 로고
    • The characterization of amino acid sequences in proteins by statistical methods
    • Zimmerman JM, Eliezer N, Simha R (1968) The characterization of amino acid sequences in proteins by statistical methods. J Theor Biol 21: 170-201.
    • (1968) J Theor Biol , vol.21 , pp. 170-201
    • Zimmerman, J.M.1    Eliezer, N.2    Simha, R.3
  • 47
    • 56649112638 scopus 로고    scopus 로고
    • Implications of N and C-terminal proximity for protein folding
    • Christopher JA, Baldwin TO (1996) Implications of N and C-terminal proximity for protein folding. Proc Natl Acad Sci USA 102: 1053-1158.
    • (1996) Proc Natl Acad Sci USA , vol.102 , pp. 1053-1158
    • Christopher, J.A.1    Baldwin, T.O.2
  • 48
    • 0036498862 scopus 로고    scopus 로고
    • Functional diversity of protein C-termini: More than zipcoding
    • Chung JJ, Shikano S, Hanyu Y, Li M (2002) Functional diversity of protein C-termini: more than zipcoding. Trends Cell Biol 12: 146-150.
    • (2002) Trends Cell Biol , vol.12 , pp. 146-150
    • Chung, J.J.1    Shikano, S.2    Hanyu, Y.3    Li, M.4
  • 49
    • 33846661178 scopus 로고    scopus 로고
    • A tale of two tails: Why are terminal residues of proteins exposed?
    • Jacob E, Unger R (2006) A tale of two tails: why are terminal residues of proteins exposed? Bioinformatics 23: e225-e230.
    • (2006) Bioinformatics , vol.23
    • Jacob, E.1    Unger, R.2
  • 50
    • 33846945701 scopus 로고    scopus 로고
    • Carbonyl reductases: The complex relationships of mammalian carbonyl- and quinone-reducing enzymes and their role in physiology
    • Oppermann U (2007) Carbonyl reductases: The complex relationships of mammalian carbonyl- and quinone-reducing enzymes and their role in physiology. Annu Rev Pharmacol Toxicol 47: 293-322.
    • (2007) Annu Rev Pharmacol Toxicol , vol.47 , pp. 293-322
    • Oppermann, U.1
  • 51
    • 33645963469 scopus 로고    scopus 로고
    • Multiplicity of mammalian reductases for xenobiotic carbonyl compounds
    • Matsunaga T, Shintani S, Hara A (2006) Multiplicity of mammalian reductases for xenobiotic carbonyl compounds. Drug Metab Pharmacokinet 21: 1-18.
    • (2006) Drug Metab Pharmacokinet , vol.21 , pp. 1-18
    • Matsunaga, T.1    Shintani, S.2    Hara, A.3
  • 52
    • 0035947598 scopus 로고    scopus 로고
    • Porcine carbonyl reductase. structural basis for a functional monomer in short chain dehydrogenases/reductases
    • Ghosh D, Sawicki M, Pletnev V, Erman M, Ohno S, et al. (2001) Porcine carbonyl reductase. structural basis for a functional monomer in short chain dehydrogenases/reductases. J Biol Chem 276: 18457-18463.
    • (2001) J Biol Chem , vol.276 , pp. 18457-18463
    • Ghosh, D.1    Sawicki, M.2    Pletnev, V.3    Erman, M.4    Ohno, S.5
  • 53
    • 0028773893 scopus 로고
    • The refined three-dimensional structure of 3 alpha, 20 beta-hydroxysteroid dehydrogenase and possible roles of the residues conserved in short-chain dehydrogenases
    • Ghosh D, Wawrzak Z, Weeks C, Duax W, Erman M (1994) The refined three-dimensional structure of 3 alpha, 20 beta-hydroxysteroid dehydrogenase and possible roles of the residues conserved in short-chain dehydrogenases. Structure 2: 629-640.
    • (1994) Structure , vol.2 , pp. 629-640
    • Ghosh, D.1    Wawrzak, Z.2    Weeks, C.3    Duax, W.4    Erman, M.5
  • 54
    • 0030000879 scopus 로고    scopus 로고
    • Crystal structures of the binary and ternary complexes of 7 alpha-hydroxysteroid dehydrogenase from Escherichia coli
    • Tanaka N, Nonaka T, Tanabe T, Yoshimoto T, Tsuru D, et al. (1996) Crystal structures of the binary and ternary complexes of 7 alpha-hydroxysteroid dehydrogenase from Escherichia coli. Biochemistry 35: 7715-7730.
    • (1996) Biochemistry , vol.35 , pp. 7715-7730
    • Tanaka, N.1    Nonaka, T.2    Tanabe, T.3    Yoshimoto, T.4    Tsuru, D.5
  • 56
    • 13544253732 scopus 로고    scopus 로고
    • Functional significance of a natural allelic variant of human carbonyl reductase 3 (CBR3)
    • Sukhwinder SL, Ghosh D, Blanco JG (2005) Functional significance of a natural allelic variant of human carbonyl reductase 3 (CBR3). Drug Metab Dispos 33: 254-257.
    • (2005) Drug Metab Dispos , vol.33 , pp. 254-257
    • Sukhwinder, S.L.1    Ghosh, D.2    Blanco, J.G.3
  • 57
    • 0036701963 scopus 로고    scopus 로고
    • Phylogenetic analysis of Salmonella, Shigella, and Escherichia coli strains on the basis of the gyrB gene sequence
    • Fukushima M, Kakinuma K, Kawaguchi R (2002) Phylogenetic analysis of Salmonella, Shigella, and Escherichia coli strains on the basis of the gyrB gene sequence. J Clin Microbiol 40: 2779-2785.
    • (2002) J Clin Microbiol , vol.40 , pp. 2779-2785
    • Fukushima, M.1    Kakinuma, K.2    Kawaguchi, R.3
  • 59
    • 3042565153 scopus 로고    scopus 로고
    • Evidence for two different electron transfer pathways in the same enzyme, nitrate reductase a from Escherichia coli
    • Giordani R, Buc J (2004) Evidence for two different electron transfer pathways in the same enzyme, nitrate reductase a from Escherichia coli. Eur J Biochem 271: 2400-2407.
    • (2004) Eur J Biochem , vol.271 , pp. 2400-2407
    • Giordani, R.1    Buc, J.2
  • 60
    • 0041318860 scopus 로고    scopus 로고
    • Insights into the respiratory electron transfer pathway from the structure of nitrate reductase A
    • Bertero MG, Rothery RA, Palak M, Hou C, Lim D, et al. (2003) Insights into the respiratory electron transfer pathway from the structure of nitrate reductase A. Nat Struct Biol 10: 681-687.
    • (2003) Nat Struct Biol , vol.10 , pp. 681-687
    • Bertero, M.G.1    Rothery, R.A.2    Palak, M.3    Hou, C.4    Lim, D.5
  • 61
    • 33845954688 scopus 로고    scopus 로고
    • Crystal structure of aminopeptidase N (proteobacteria alanyl aminopeptidase) from Escherichia coli and conformational change of methionine 260 involved in substrate recognition
    • Ito K, Nakajima Y, Onohara Y, Takeo M, Nakashima K, et al. (2006) Crystal structure of aminopeptidase N (proteobacteria alanyl aminopeptidase) from Escherichia coli and conformational change of methionine 260 involved in substrate recognition. J Biol Chem 281: 33664-33676.
    • (2006) J Biol Chem , vol.281 , pp. 33664-33676
    • Ito, K.1    Nakajima, Y.2    Onohara, Y.3    Takeo, M.4    Nakashima, K.5
  • 62
    • 0035476623 scopus 로고    scopus 로고
    • Crystal structure of human protein kinase CK2: Insights into basic properties of the CK2 holoenzyme
    • Niefind K, Guerra B, Ermakowa I, Issinger OG (2001) Crystal structure of human protein kinase CK2: insights into basic properties of the CK2 holoenzyme. EMBO J 20: 5320-5331.
    • (2001) EMBO J , vol.20 , pp. 5320-5331
    • Niefind, K.1    Guerra, B.2    Ermakowa, I.3    Issinger, O.G.4
  • 64
    • 38549153853 scopus 로고    scopus 로고
    • Human PAML browser: A database of positive selection on human genes using phylogenetic methods
    • Nickel GC, Tefft D, Adams MD (2008) Human PAML browser: a database of positive selection on human genes using phylogenetic methods. Nucleic Acids Res 36: D800-D808.
    • (2008) Nucleic Acids Res , vol.36
    • Nickel, G.C.1    Tefft, D.2    Adams, M.D.3
  • 65
    • 19944373422 scopus 로고    scopus 로고
    • Tertiary windowing to detect positive diversifying selection
    • Berglund AC, Wallner B, Elofsson A, Liberles DA (2005) Tertiary windowing to detect positive diversifying selection. J Mol Evol 60: 499-504.
    • (2005) J Mol Evol , vol.60 , pp. 499-504
    • Berglund, A.C.1    Wallner, B.2    Elofsson, A.3    Liberles, D.A.4
  • 66
    • 33747863300 scopus 로고    scopus 로고
    • SWAKK: A web server for detecting positive selection in proteins using a sliding window substitution rate analysis
    • Liang H, Zhou W, Landweber LF (2006) SWAKK: a web server for detecting positive selection in proteins using a sliding window substitution rate analysis. Nucleic Acids Res 34: W382-W384.
    • (2006) Nucleic Acids Res , vol.34
    • Liang, H.1    Zhou, W.2    Landweber, L.F.3
  • 67
    • 0028109886 scopus 로고
    • Conservation and prediction of solvent accessibility in protein families
    • Rost B, Sander C (1994) Conservation and prediction of solvent accessibility in protein families. Proteins 20: 216-226.
    • (1994) Proteins , vol.20 , pp. 216-226
    • Rost, B.1    Sander, C.2
  • 68
    • 0029885547 scopus 로고    scopus 로고
    • Predicting solvent accessibility: Higher accuracy using Bayesian statistics and optimized residue substitution classes
    • Thompson MJ, Goldstein RA (1996) Predicting solvent accessibility: higher accuracy using Bayesian statistics and optimized residue substitution classes. Proteins 25: 38-47.
    • (1996) Proteins , vol.25 , pp. 38-47
    • Thompson, M.J.1    Goldstein, R.A.2
  • 69
    • 0036568293 scopus 로고    scopus 로고
    • Prediction of coordination number and relative solvent accessibility in proteins
    • Pollastri G, Baldi P, Fariselli P, Casadio R (2002) Prediction of coordination number and relative solvent accessibility in proteins. Proteins 47: 142-153.
    • (2002) Proteins , vol.47 , pp. 142-153
    • Pollastri, G.1    Baldi, P.2    Fariselli, P.3    Casadio, R.4
  • 70
    • 4043052866 scopus 로고    scopus 로고
    • Accurate prediction of solvent accessibility using neural networks based regression
    • Adamczak R, Porollo A, Meller J (2004) Accurate prediction of solvent accessibility using neural networks based regression. Proteins 56: 753-767.
    • (2004) Proteins , vol.56 , pp. 753-767
    • Adamczak, R.1    Porollo, A.2    Meller, J.3
  • 71
    • 14644440766 scopus 로고    scopus 로고
    • Prediction of protein relative solvent accessibility with a two-stage SVM approach
    • Nguyen MN, Rajapakse JC (2005) Prediction of protein relative solvent accessibility with a two-stage SVM approach. Proteins 59: 30-37.
    • (2005) Proteins , vol.59 , pp. 30-37
    • Nguyen, M.N.1    Rajapakse, J.C.2
  • 72
    • 23344451687 scopus 로고    scopus 로고
    • Structure, function, and evolution of transient and obligate protein-protein interactions
    • Mintseris J, Weng Z (2005) Structure, function, and evolution of transient and obligate protein-protein interactions. Proc Natl Acad Sci USA 102: 10930-10935.
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 10930-10935
    • Mintseris, J.1    Weng, Z.2
  • 73
    • 35748929071 scopus 로고    scopus 로고
    • Structural mapping of protein interactions reveals differences in evolutionary pressures correlated to mRNA level and protein abundance
    • Eames M, Kortemme T (2007) Structural mapping of protein interactions reveals differences in evolutionary pressures correlated to mRNA level and protein abundance. Structure 15: 1442-1451.
    • (2007) Structure , vol.15 , pp. 1442-1451
    • Eames, M.1    Kortemme, T.2
  • 74
    • 0029913807 scopus 로고    scopus 로고
    • An evolutionary trace method defines binding surfaces common to protein families
    • Lichtarge O, Bourne HR, Cohen FE (1996) An evolutionary trace method defines binding surfaces common to protein families. J Mol Biol 257: 342-358.
    • (1996) J Mol Biol , vol.257 , pp. 342-358
    • Lichtarge, O.1    Bourne, H.R.2    Cohen, F.E.3
  • 75
    • 0027152131 scopus 로고
    • ζ-crystallin versus other members of the alcohol dehydrogenase super-family
    • Jörnvall H, Persson B, Du Bois GC, Lavers GC, Chen JH, et al. (1993) ζ-crystallin versus other members of the alcohol dehydrogenase super-family. FEBS Lett 322: 240-244.
    • (1993) FEBS Lett , vol.322 , pp. 240-244
    • Jörnvall, H.1    Persson, B.2    Du Bois, G.C.3    Lavers, G.C.4    Chen, J.H.5
  • 76
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: Multiple sequence alignment with high accuracy and high throughput
    • Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792-1797.
    • (2004) Nucleic Acids Res , vol.32 , pp. 1792-1797
    • Edgar, R.C.1
  • 77
    • 0036084143 scopus 로고    scopus 로고
    • GTOP: A database of protein structures predicted from genome sequence
    • Kawabata T, Fukuchi S, Homma K, Ota M, Araki J, et al. (2002) GTOP: a database of protein structures predicted from genome sequence. Nucleic Acids Res 30: 294-298.
    • (2002) Nucleic Acids Res , vol.30 , pp. 294-298
    • Kawabata, T.1    Fukuchi, S.2    Homma, K.3    Ota, M.4    Araki, J.5
  • 78
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch W, 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


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