메뉴 건너뛰기




Volumn 2008, Issue 4, 2008, Pages 237-246

Why should we care about molecular coevolution?

Author keywords

Molecular coevolution; Mutual Information Content; Non parametric methods; Parametric methods; Protein protein interactions

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; COEVOLUTION; COVARIANCE; FUNCTIONAL GENOMICS; GENE EXPRESSION; GENE MUTATION; GENETIC VARIABILITY; MATHEMATICAL COMPUTING; MOLECULAR EVOLUTION; NONPARAMETRIC TEST; PARAMETRIC TEST; PHYLOGENETIC TREE; PHYLOGENY; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS; STOCHASTIC MODEL; STRUCTURAL GENOMICS;

EID: 41049083552     PISSN: None     EISSN: 11769343     Source Type: Journal    
DOI: None     Document Type: Article
Times cited : (53)

References (79)
  • 1
    • 0033977832 scopus 로고    scopus 로고
    • Correlations among amino acid sites in bBLH protein domains: An information theoretic analysis
    • Atchley, W.R., Wollenberg, K.R., Fitch, W.M., Terhalle, W. and Dress, A.W. 2000. Correlations among amino acid sites in bBLH protein domains: an information theoretic analysis. Mol. Biol. Evol., 17:164-78.
    • (2000) Mol. Biol. Evol , vol.17 , pp. 164-178
    • Atchley, W.R.1    Wollenberg, K.R.2    Fitch, W.M.3    Terhalle, W.4    Dress, A.W.5
  • 2
    • 0030707656 scopus 로고    scopus 로고
    • Structural plasticity in a remodeled protein-protein interface
    • Atwell, S., Ultsch, M., de Vos, A.M. and Wells, J.A. 1997. Structural plasticity in a remodeled protein-protein interface. Science, 278:1125-8.
    • (1997) Science , vol.278 , pp. 1125-1128
    • Atwell, S.1    Ultsch, M.2    de Vos, A.M.3    Wells, J.A.4
  • 3
  • 4
    • 0034635955 scopus 로고    scopus 로고
    • A statistical mechanical method to optimize energy functions for protein folding
    • Bastolla, U., Vendruscolo, M. and Knapp, E.W. 2000. A statistical mechanical method to optimize energy functions for protein folding. Proc. Natl. Acad. Sci. U.S.A., 97:3977-81.
    • (2000) Proc. Natl. Acad. Sci. U.S.A , vol.97 , pp. 3977-3981
    • Bastolla, U.1    Vendruscolo, M.2    Knapp, E.W.3
  • 6
    • 20444426807 scopus 로고    scopus 로고
    • Networks of coevolving sites in structural and functional domains of serpin proteins
    • Buck, M.J. and Atchley, W. R. 2005. Networks of coevolving sites in structural and functional domains of serpin proteins. Mol. Biol. Evol., 22:1627-34.
    • (2005) Mol. Biol. Evol , vol.22 , pp. 1627-1634
    • Buck, M.J.1    Atchley, W.R.2
  • 8
    • 33748701649 scopus 로고    scopus 로고
    • Detecting functional modules in the yeast protein-protein interaction network
    • Chen, J. and Yuan, B. 2006. Detecting functional modules in the yeast protein-protein interaction network. Bioinformatics, 22:2283-90.
    • (2006) Bioinformatics , vol.22 , pp. 2283-2290
    • Chen, J.1    Yuan, B.2
  • 9
    • 33745622668 scopus 로고    scopus 로고
    • An effective structure learning method for constructing gene networks
    • Chen, X-W., Anantha, G. and Wang, X. 2006. An effective structure learning method for constructing gene networks. Bioinformatics, 22:1367-74.
    • (2006) Bioinformatics , vol.22 , pp. 1367-1374
    • Chen, X.-W.1    Anantha, G.2    Wang, X.3
  • 10
    • 28444463255 scopus 로고    scopus 로고
    • Robust signals of coevolution of interacting residues in mammalian proteomes identified by phylogeny-aided structural analysis
    • Choi, S.S., Li, W. and Lahn, B.T. 2005. Robust signals of coevolution of interacting residues in mammalian proteomes identified by phylogeny-aided structural analysis. Nat. Genet., 37:1367-71.
    • (2005) Nat. Genet , vol.37 , pp. 1367-1371
    • Choi, S.S.1    Li, W.2    Lahn, B.T.3
  • 11
    • 0028832687 scopus 로고
    • Covariation residues in the homeodomain sequence family
    • Clarke, N.D. 1995. Covariation residues in the homeodomain sequence family. Protein Sci., 4:2269-78.
    • (1995) Protein Sci , vol.4 , pp. 2269-2278
    • Clarke, N.D.1
  • 12
    • 33744940805 scopus 로고    scopus 로고
    • Adaptative Covariation between the coat and the movement proteins of Prunus Necrotic Ringspot Virus
    • Codoñer, F.M., Fares, M.A. and Elena, S.F. 2006. Adaptative Covariation between the coat and the movement proteins of Prunus Necrotic Ringspot Virus. J. Virol., 80:5833-40.
    • (2006) J. Virol , vol.80 , pp. 5833-5840
    • Codoñer, F.M.1    Fares, M.A.2    Elena, S.F.3
  • 13
    • 0032169271 scopus 로고    scopus 로고
    • Conservation of gene order: A fingerprint of proteins that physically interact
    • Dandekar, T., Snel, B., Huynen, M. and Bork, P. 1998. Conservation of gene order: a fingerprint of proteins that physically interact. Trends Biochem. Sci., 23:324-8.
    • (1998) Trends Biochem. Sci , vol.23 , pp. 324-328
    • Dandekar, T.1    Snel, B.2    Huynen, M.3    Bork, P.4
  • 14
    • 0041358614 scopus 로고    scopus 로고
    • Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages
    • Date, S.V. and Marcotte, E.M. 2003. Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages. Nature Biotechnol., 21:1055-62.
    • (2003) Nature Biotechnol , vol.21 , pp. 1055-1062
    • Date, S.V.1    Marcotte, E.M.2
  • 15
    • 0036799752 scopus 로고    scopus 로고
    • Inferring Domain-Domain interactions from protein-protein interactions
    • Deng, M., Mehta, S.; Sun, F. and Chen, T. 2002. Inferring Domain-Domain interactions from protein-protein interactions. Genome Research, 12:1540-8.
    • (2002) Genome Research , vol.12 , pp. 1540-1548
    • Deng, M.1    Mehta, S.2    Sun, F.3    Chen, T.4
  • 16
    • 84860533518 scopus 로고    scopus 로고
    • Detecting coevolving amino acid sites using Bayesian mutational mapping
    • Dimmic, M.W., Hubisz, M.J., Bustamante, C.D. and Nielsen, R. 2005. Detecting coevolving amino acid sites using Bayesian mutational mapping. Bioinformatics, 21:i126-35.
    • (2005) Bioinformatics , vol.21 , Issue.I126-35
    • Dimmic, M.W.1    Hubisz, M.J.2    Bustamante, C.D.3    Nielsen, R.4
  • 17
    • 0026736363 scopus 로고
    • Determination of eukaryotic protein coding regions using neutral networks and information theory
    • Farber, R., Lapedes, A. and Sirotkin, K. 1992. Determination of eukaryotic protein coding regions using neutral networks and information theory. J. Mol. Biol., 226:471-9.
    • (1992) J. Mol. Biol , vol.226 , pp. 471-479
    • Farber, R.1    Lapedes, A.2    Sirotkin, K.3
  • 18
    • 33750998062 scopus 로고    scopus 로고
    • Computational and statistical methods to explore the various dimensions of protein evolution
    • Fares, M.A. 2006. Computational and statistical methods to explore the various dimensions of protein evolution. Curr. Bioinf., 1:207-17.
    • (2006) Curr. Bioinf , vol.1 , pp. 207-217
    • Fares, M.A.1
  • 19
    • 33751017993 scopus 로고    scopus 로고
    • CAPS: Coevolution Analysis using Protein Sequences
    • Fares, M.A. and McNally, D. 2006. CAPS: Coevolution Analysis using Protein Sequences. Bioinformatics, 22:2821-2.
    • (2006) Bioinformatics , vol.22 , pp. 2821-2822
    • Fares, M.A.1    McNally, D.2
  • 20
    • 33744457709 scopus 로고    scopus 로고
    • A novel method for detecting intra-molecular coevolution: Adding a further dimension to selective constraints analyses
    • Fares, M.A. and Travers, S.A.A. 2006. A novel method for detecting intra-molecular coevolution: adding a further dimension to selective constraints analyses. Genetics, 173:9-23.
    • (2006) Genetics , vol.173 , pp. 9-23
    • Fares, M.A.1    Travers, S.A.A.2
  • 21
    • 0022203256 scopus 로고
    • Phylogenies and the comparative method
    • Felsenstein, J. 1985. Phylogenies and the comparative method. Am. Nat., 15:1-15.
    • (1985) Am. Nat , vol.15 , pp. 1-15
    • Felsenstein, J.1
  • 22
    • 0015162378 scopus 로고
    • Rate of change of concomitantly variable codons
    • Fitch, W.M. 1971. Rate of change of concomitantly variable codons. J. Mol. Evol., 1:84-96.
    • (1971) J. Mol. Evol , vol.1 , pp. 84-96
    • Fitch, W.M.1
  • 23
    • 0014860857 scopus 로고    scopus 로고
    • Fitch, W.M. and Markowitz, E. 1970. An improved method for determining codon variability in a gene and its application to the rate of fixation of mutations in evolution Biochem. Genetics, 4:579-3.
    • Fitch, W.M. and Markowitz, E. 1970. An improved method for determining codon variability in a gene and its application to the rate of fixation of mutations in evolution Biochem. Genetics, 4:579-3.
  • 24
    • 3042842115 scopus 로고    scopus 로고
    • Fodor, A. A and Aldrich, R. W. 2004. Influence of conservation on calculations of amino acid covariance in multiple sequence alignments. Proteins, 56:211-21.
    • Fodor, A. A and Aldrich, R. W. 2004. Influence of conservation on calculations of amino acid covariance in multiple sequence alignments. Proteins, 56:211-21.
  • 26
    • 0036145469 scopus 로고    scopus 로고
    • Persistently conserved positions in structurally similar, sequences dissimilar proteins: Roles in preserving protein fold and function
    • Friedber, I. and Margalit, H. 2002. Persistently conserved positions in structurally similar, sequences dissimilar proteins: roles in preserving protein fold and function. Protein Sci., 11:350-60.
    • (2002) Protein Sci , vol.11 , pp. 350-360
    • Friedber, I.1    Margalit, H.2
  • 27
    • 0030249746 scopus 로고    scopus 로고
    • The coevolution of gene family trees
    • Fryxell, K.J. 1996. The coevolution of gene family trees. Trends Genet., 12:364-9.
    • (1996) Trends Genet , vol.12 , pp. 364-369
    • Fryxell, K.J.1
  • 28
    • 0036301488 scopus 로고    scopus 로고
    • Detecting compensatory covariation signals in protein evolution using reconstructed ancestral sequences
    • Fukami-Kobayashi, K., Schreiber, D.R. and Benner, S.A. 2002. Detecting compensatory covariation signals in protein evolution using reconstructed ancestral sequences. J. Mol. Biol., 319:729-43.
    • (2002) J. Mol. Biol , vol.319 , pp. 729-743
    • Fukami-Kobayashi, K.1    Schreiber, D.R.2    Benner, S.A.3
  • 29
    • 18544362952 scopus 로고    scopus 로고
    • Mutual information in protein multiple alignments reveals two classes of coevolving positions
    • Gloor, G.B., Martin, L.C., Wahl, L.M. and Dunn, S.D. 2005. Mutual information in protein multiple alignments reveals two classes of coevolving positions. Biochemistry, 44:7156-65.
    • (2005) Biochemistry , vol.44 , pp. 7156-7165
    • Gloor, G.B.1    Martin, L.C.2    Wahl, L.M.3    Dunn, S.D.4
  • 30
    • 0028295169 scopus 로고
    • Correlated mutations and residue contacts in proteins
    • Göbel, U., Sander, C., Schneider, R. and Valencia, A. 1994. Correlated mutations and residue contacts in proteins. Proteins, 18:309-17.
    • (1994) Proteins , vol.18 , pp. 309-317
    • Göbel, U.1    Sander, C.2    Schneider, R.3    Valencia, A.4
  • 32
    • 0036435908 scopus 로고    scopus 로고
    • Coevolutionary analysis reveals insights into protein-protein interactions
    • Goh Ch, S. and Cohen, F.E. 2002. Coevolutionary analysis reveals insights into protein-protein interactions. J. Mol. Biol., 324:177-92.
    • (2002) J. Mol. Biol , vol.324 , pp. 177-192
    • Goh Ch, S.1    Cohen, F.E.2
  • 33
    • 4043170491 scopus 로고    scopus 로고
    • Protein contact prediction using paterns of correlation
    • Hamilton, N., Burrage, K., Ragan, M.A. and Huber, T. 2004. Protein contact prediction using paterns of correlation. Proteins, 56:679-84.
    • (2004) Proteins , vol.56 , pp. 679-684
    • Hamilton, N.1    Burrage, K.2    Ragan, M.A.3    Huber, T.4
  • 34
    • 0141571239 scopus 로고    scopus 로고
    • Covariation of amino acid positions in HIV-protease
    • Hoffman, N.G., Schiffer, C.A. and Swanstrom, R. 2003. Covariation of amino acid positions in HIV-protease. Virology, 314:536-48.
    • (2003) Virology , vol.314 , pp. 536-548
    • Hoffman, N.G.1    Schiffer, C.A.2    Swanstrom, R.3
  • 35
    • 0023764283 scopus 로고
    • Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection
    • Hughes, A. L and Nei, M. 1988. Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection. Nature, 335:167-170.
    • (1988) Nature , vol.335 , pp. 167-170
    • Hughes, A.L.1    Nei, M.2
  • 36
    • 25444465885 scopus 로고    scopus 로고
    • Species-specific analysis of protein sequence motifs using mutual information
    • Hummel, J., Keshvari, N., Weckwerth, W. and Selbig, J. 2005. Species-specific analysis of protein sequence motifs using mutual information. BMC Bioinformatics, 6:164-70.
    • (2005) BMC Bioinformatics , vol.6 , pp. 164-170
    • Hummel, J.1    Keshvari, N.2    Weckwerth, W.3    Selbig, J.4
  • 37
    • 0000371962 scopus 로고
    • When is it coevolution?
    • Janzen, D.H. 1980. When is it coevolution?. Evolution, 34:611-2.
    • (1980) Evolution , vol.34 , pp. 611-612
    • Janzen, D.H.1
  • 38
    • 33748333117 scopus 로고    scopus 로고
    • Coevolutionary analysis of domains in interacting proteins reveals insights into domain-domain interactions mediating protein-protein interactions
    • Jothi, R., Cherukuri, P.F., Tansneem, A. and Przytycka, T.M. 2006. Coevolutionary analysis of domains in interacting proteins reveals insights into domain-domain interactions mediating protein-protein interactions. J. Mol. Biol., 362:861-75.
    • (2006) J. Mol. Biol , vol.362 , pp. 861-875
    • Jothi, R.1    Cherukuri, P.F.2    Tansneem, A.3    Przytycka, T.M.4
  • 39
    • 0037311772 scopus 로고    scopus 로고
    • Visualization and analysis of protein interactions
    • Ju, B.-H., Park, B., Park, J.H. and Han, K. 2003. Visualization and analysis of protein interactions. Bioinformatics, 19:317-8.
    • (2003) Bioinformatics , vol.19 , pp. 317-318
    • Ju, B.-H.1    Park, B.2    Park, J.H.3    Han, K.4
  • 40
    • 2442646432 scopus 로고    scopus 로고
    • Large-scale coevolution analysis of protein structural interlogues using the global protein structural interactome map (PSIMAP)
    • Kim, W.K., Bolser, D.M. and Park, J.H. 2004. Large-scale coevolution analysis of protein structural interlogues using the global protein structural interactome map (PSIMAP). Bioinformatics, 20:1138-50.
    • (2004) Bioinformatics , vol.20 , pp. 1138-1150
    • Kim, W.K.1    Bolser, D.M.2    Park, J.H.3
  • 42
    • 33644845048 scopus 로고    scopus 로고
    • Locally defined protein phylogenetic profiles reveal previously missed protein interactions and functional relationships
    • Kim, Y. and Subramaniam, S. 2006. Locally defined protein phylogenetic profiles reveal previously missed protein interactions and functional relationships. Proteins, 62:1115-24.
    • (2006) Proteins , vol.62 , pp. 1115-1124
    • Kim, Y.1    Subramaniam, S.2
  • 43
    • 0014421064 scopus 로고
    • Evolutionary rate at the molecular level
    • Kimura, M. 1968. Evolutionary rate at the molecular level. Nature, 217:624-626.
    • (1968) Nature , vol.217 , pp. 624-626
    • Kimura, M.1
  • 44
    • 0027297096 scopus 로고
    • Covariation of mutations in the V3 loop of human immunodeficiency virus type 1 envelope protein: An information theoretic analysis
    • Korber, B.T., Farber, R.M., Wolpert, D.H. and Lapedes, A.S. 1993. Covariation of mutations in the V3 loop of human immunodeficiency virus type 1 envelope protein: an information theoretic analysis. Proc. Natl. Acad. Sci. U.S.A., 90:7176-80.
    • (1993) Proc. Natl. Acad. Sci. U.S.A , vol.90 , pp. 7176-7180
    • Korber, B.T.1    Farber, R.M.2    Wolpert, D.H.3    Lapedes, A.S.4
  • 46
    • 27944458910 scopus 로고    scopus 로고
    • Using information theory to search for co-evolving residues in proteins
    • Martin, L.C., Gloor, G.B., Dunn, S.D. and Wahl, L.M. 2005. Using information theory to search for co-evolving residues in proteins. Bioinformatics, 21:4116-24.
    • (2005) Bioinformatics , vol.21 , pp. 4116-4124
    • Martin, L.C.1    Gloor, G.B.2    Dunn, S.D.3    Wahl, L.M.4
  • 47
    • 23344451687 scopus 로고    scopus 로고
    • Structure function and evolution of transient and obligate protein-protein interactions
    • Mintseris, J. and Weng, Z. 2005. Structure function and evolution of transient and obligate protein-protein interactions. Proc. Natl. Acad. Sci. U.S.A., 102:10930-5.
    • (2005) Proc. Natl. Acad. Sci. U.S.A , vol.102 , pp. 10930-10935
    • Mintseris, J.1    Weng, Z.2
  • 48
    • 0345062357 scopus 로고    scopus 로고
    • Universally conserved positions in protein folds: Reading evolutionary signals about stability, folding kinetics and function
    • Mirny, L.A. and Shakhnovich, E.L. 1999. Universally conserved positions in protein folds: reading evolutionary signals about stability, folding kinetics and function. J. Mol. Biol., 291:177-96.
    • (1999) J. Mol. Biol , vol.291 , pp. 177-196
    • Mirny, L.A.1    Shakhnovich, E.L.2
  • 50
    • 0028125904 scopus 로고
    • How frequent are correlated changes in families of protein sequences?
    • Neher, E. 1994. How frequent are correlated changes in families of protein sequences?. Proc. Natl. Acad. Sci. U.S.A., 91:98-102.
    • (1994) Proc. Natl. Acad. Sci. U.S.A , vol.91 , pp. 98-102
    • Neher, E.1
  • 51
  • 52
    • 0037020282 scopus 로고    scopus 로고
    • Correlated mutation apalyses on very large sequence families
    • Olivera, L., Paiva, A.C.M and Vriend, G. 2002. Correlated mutation apalyses on very large sequence families. ChemBioChem., 3:1010-7.
    • (2002) ChemBioChem , vol.3 , pp. 1010-1017
    • Olivera, L.1    Paiva, A.C.M.2    Vriend, G.3
  • 53
    • 0041418225 scopus 로고    scopus 로고
    • Identification of functionally conserved residues with the use of entropy-variability plots
    • Oliveira, L., Paiva, A.C.M, Paiva, G. and Vriend, G. 2003. Identification of functionally conserved residues with the use of entropy-variability plots. Proteins, 52:544-52.
    • (2003) Proteins , vol.52 , pp. 544-552
    • Oliveira, L.1    Paiva, A.C.M.2    Paiva, G.3    Vriend, G.4
  • 54
    • 0028097770 scopus 로고
    • Detecting correlated evolution on phylogenies: A general method for the comparative analysis of discrete characters
    • Pagel, M. 1994. Detecting correlated evolution on phylogenies: a general method for the comparative analysis of discrete characters. Proc. Roy. Soc. London ser. B., 255:37-45.
    • (1994) Proc. Roy. Soc. London ser. B , vol.255 , pp. 37-45
    • Pagel, M.1
  • 55
    • 0035177259 scopus 로고    scopus 로고
    • Similarity of phylogenetic trees as indicator of protein-protein interaction
    • Pazos, F. and Valencia, A. 2001. Similarity of phylogenetic trees as indicator of protein-protein interaction. Protein Engineering, 14:609-14.
    • (2001) Protein Engineering , vol.14 , pp. 609-614
    • Pazos, F.1    Valencia, A.2
  • 56
    • 0036568319 scopus 로고    scopus 로고
    • In silico two-hybrid system for Selection of physically interacting protein pairs
    • Pazos, F. and Valencia, A. 2002. In silico two-hybrid system for Selection of physically interacting protein pairs. Proteins, 47:219-27.
    • (2002) Proteins , vol.47 , pp. 219-227
    • Pazos, F.1    Valencia, A.2
  • 57
    • 0030821675 scopus 로고    scopus 로고
    • Correlated mutations contain information-about protein-protein interaction
    • Pazos, F., Helmer-Citterich, M., Ausiello, G. and Valencia, A. 1997. Correlated mutations contain information-about protein-protein interaction. J. Mol. Biol., 271:511-23.
    • (1997) J. Mol. Biol , vol.271 , pp. 511-523
    • Pazos, F.1    Helmer-Citterich, M.2    Ausiello, G.3    Valencia, A.4
  • 58
    • 24644502565 scopus 로고    scopus 로고
    • Assessing protein coevolution in the context of the tree life assists in the prediction of the interactome
    • Pazos, F., Ranea, J.A.G, Juan, D. and Strenberg, M.J.E. 2005. Assessing protein coevolution in the context of the tree life assists in the prediction of the interactome. J. Mol. Biol., 352:1002-15.
    • (2005) J. Mol. Biol , vol.352 , pp. 1002-1015
    • Pazos, F.1    Ranea, J.A.G.2    Juan, D.3    Strenberg, M.J.E.4
  • 59
    • 32144442848 scopus 로고    scopus 로고
    • Prediction of functional specificity determinants from protein sequeces using log-likelihood ratios
    • Pei, J., Cai, W., Kinc, L.N. and Grishin, N.V. 2006. Prediction of functional specificity determinants from protein sequeces using log-likelihood ratios. Bioinformatics, 22:164-71.
    • (2006) Bioinformatics , vol.22 , pp. 164-171
    • Pei, J.1    Cai, W.2    Kinc, L.N.3    Grishin, N.V.4
  • 61
    • 0030743758 scopus 로고    scopus 로고
    • Effectiveness of correlation analysis in identifying protein residues undergoing correlated evolution
    • Pollock, D.D. and Taylor, W.R. 1997. Effectiveness of correlation analysis in identifying protein residues undergoing correlated evolution. Protein Engineering, 6:647-57.
    • (1997) Protein Engineering , vol.6 , pp. 647-657
    • Pollock, D.D.1    Taylor, W.R.2
  • 62
    • 0033582946 scopus 로고    scopus 로고
    • Coevolving protein residues: Maximum likelihood identification and relationship to structure
    • Pollock, D.D., Taylor, W.R. and Goldman, N. 1999. Coevolving protein residues: maximum likelihood identification and relationship to structure. J. Mol. Biol., 287:187-98.
    • (1999) J. Mol. Biol , vol.287 , pp. 187-198
    • Pollock, D.D.1    Taylor, W.R.2    Goldman, N.3
  • 63
    • 0034794239 scopus 로고    scopus 로고
    • Evaluation of a anovel method for the identification of coevolving protein residues
    • Pritchard, L., Bladon, P., Mitchell, J.M.O and Dufton, M.J. 2001. Evaluation of a anovel method for the identification of coevolving protein residues. Protein Engineering, 14:549-55.
    • (2001) Protein Engineering , vol.14 , pp. 549-555
    • Pritchard, L.1    Bladon, P.2    Mitchell, J.M.O.3    Dufton, M.J.4
  • 64
    • 0037436412 scopus 로고    scopus 로고
    • Exploiting the coevolution of interacting proteins to discover interaction specificity
    • Ramani, A.K. and Marcotte, E.M. 2003. Exploiting the coevolution of interacting proteins to discover interaction specificity. J. Mol. Biol., 327:273-84.
    • (2003) J. Mol. Biol , vol.327 , pp. 273-284
    • Ramani, A.K.1    Marcotte, E.M.2
  • 65
    • 0029091043 scopus 로고
    • Estimating substitution rates in ribosomal RNA genes
    • Rzhetsky, A. 1995. Estimating substitution rates in ribosomal RNA genes. Mol. Biol. Evol., 141:771-83.
    • (1995) Mol. Biol. Evol , vol.141 , pp. 771-783
    • Rzhetsky, A.1
  • 66
    • 0027288463 scopus 로고
    • The HSSP data base of protein structure-sequence alignments
    • Sander, C. and Schneider, R. 1993. The HSSP data base of protein structure-sequence alignments. Nucleic Acid Res., 21:3105-9.
    • (1993) Nucleic Acid Res , vol.21 , pp. 3105-3109
    • Sander, C.1    Schneider, R.2
  • 67
    • 0028512129 scopus 로고
    • A stochastic model for the evolution of autocorrelated DNA sequences
    • Schoniger, M. and von Haeseler, A. 1994. A stochastic model for the evolution of autocorrelated DNA sequences. Mol. Phylogenet Evol., 3:240-7.
    • (1994) Mol. Phylogenet Evol , vol.3 , pp. 240-247
    • Schoniger, M.1    von Haeseler, A.2
  • 68
    • 0027952860 scopus 로고
    • Compensating changes in protein multiple sequences alignments
    • Taylor, W.R. and Hatrick, K. 1994. Compensating changes in protein multiple sequences alignments. Protein Engineering, 7:341-8.
    • (1994) Protein Engineering , vol.7 , pp. 341-348
    • Taylor, W.R.1    Hatrick, K.2
  • 69
    • 0037433701 scopus 로고    scopus 로고
    • Using multiple interdependency to separate functional from phylogentic correlations in protein alignments
    • Tillier, E.R.M and Lui, T.W.H. 2003. Using multiple interdependency to separate functional from phylogentic correlations in protein alignments. Bioinformatics, 19:750-5.
    • (2003) Bioinformatics , vol.19 , pp. 750-755
    • Tillier, E.R.M.1    Lui, T.W.H.2
  • 70
    • 33646822044 scopus 로고    scopus 로고
    • Codep: Maximizing coevolutionary interdependencies to discover interacting proteins
    • Tillier, E.R., Biro, L., Li, G. and Tillo, D. 2006. Codep: maximizing coevolutionary interdependencies to discover interacting proteins. Proteins, 63:822-31.
    • (2006) Proteins , vol.63 , pp. 822-831
    • Tillier, E.R.1    Biro, L.2    Li, G.3    Tillo, D.4
  • 71
    • 34047228912 scopus 로고    scopus 로고
    • Functional coevolutionary networks of the Hsp70-Hop-Hsp90 system revealed through computational analyses
    • Ahead publication
    • Travers, S.A.A and Fares, M.A. 2007. Functional coevolutionary networks of the Hsp70-Hop-Hsp90 system revealed through computational analyses. Mol. Biol. Evol., Ahead publication.
    • (2007) Mol. Biol. Evol
    • Travers, S.A.A.1    Fares, M.A.2
  • 73
    • 41049092793 scopus 로고    scopus 로고
    • Phylogenetic methodology for detecting protein interactions
    • Ahead publication
    • Waddell, P.J., Kishino, H. and Ota, R. 2006. Phylogenetic methodology for detecting protein interactions. Mol. Biol. Evol., Ahead publication.
    • (2006) Mol. Biol. Evol
    • Waddell, P.J.1    Kishino, H.2    Ota, R.3
  • 74
    • 0042672578 scopus 로고    scopus 로고
    • Scoring and identifying organism-specific functional patterns and putative phosphorylation sites in protein sequences using mutual information
    • Weckwerth, W. and Selbig, J. 2003. Scoring and identifying organism-specific functional patterns and putative phosphorylation sites in protein sequences using mutual information. Biochemical and Biophysical Research Communications, 307:516-21.
    • (2003) Biochemical and Biophysical Research Communications , vol.307 , pp. 516-521
    • Weckwerth, W.1    Selbig, J.2
  • 75
    • 0034724418 scopus 로고    scopus 로고
    • Separation of phylogentic and functional associations in biological sequences by using the parametric bootstrap
    • Wollenberg, K.R. and Atchley, W.R. 2000. Separation of phylogentic and functional associations in biological sequences by using the parametric bootstrap. Proc. Natl. Acad. Sci. U.S.A., 97:3288-91.
    • (2000) Proc. Natl. Acad. Sci. U.S.A , vol.97 , pp. 3288-3291
    • Wollenberg, K.R.1    Atchley, W.R.2
  • 76
    • 0033609902 scopus 로고    scopus 로고
    • Evolution of protein sequences and structures
    • Wood, T.C. and Pearson, W.R. 1999. Evolution of protein sequences and structures. J. Mol. Biol., 291:977-95.
    • (1999) J. Mol. Biol , vol.291 , pp. 977-995
    • Wood, T.C.1    Pearson, W.R.2
  • 77
    • 0035986872 scopus 로고    scopus 로고
    • Functional pro iscuity of squirrel monkey growth hormone receptor toward both primate and nonprimate growth hormone
    • Yi, S., Bernat, B., Pal, G., Kossiakoff, A. and Li, W.-H. 2002. Functional pro iscuity of squirrel monkey growth hormone receptor toward both primate and nonprimate growth hormone. Mol. Biol. Evol., 19:1083-92.
    • (2002) Mol. Biol. Evol , vol.19 , pp. 1083-1092
    • Yi, S.1    Bernat, B.2    Pal, G.3    Kossiakoff, A.4    Li, W.-H.5
  • 78
    • 33749514099 scopus 로고    scopus 로고
    • Genomic analysis of the hierarchical structure of regulatory networks
    • Yu, H. and Gerstein, M. 2006. Genomic analysis of the hierarchical structure of regulatory networks. Proc. Natl. Acad. Sci. U.S.A., 103:14724-31.
    • (2006) Proc. Natl. Acad. Sci. U.S.A , vol.103 , pp. 14724-14731
    • Yu, H.1    Gerstein, M.2
  • 79
    • 0037057376 scopus 로고    scopus 로고
    • Genomic functional annotation using coevolution profiles of gene clusters
    • research0060.1-0060.9
    • Zeng, Y., Roberts, R.J. and Kasif, S. 2002. Genomic functional annotation using coevolution profiles of gene clusters. Genome Biology, 3: research0060.1-0060.9.
    • (2002) Genome Biology , vol.3
    • Zeng, Y.1    Roberts, R.J.2    Kasif, S.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.