메뉴 건너뛰기




Volumn 412, Issue 23, 2011, Pages 2486-2495

Co-evolution and information signals in biological sequences

Author keywords

Co evolution; Conservation; DNA sequences; Entropy; Evolution; Information content; Mutual information; Phylogeny; Protein sequences; Protein structures; Randomization

Indexed keywords

CO-EVOLUTION; EVOLUTION; INFORMATION CONTENT; MUTUAL INFORMATIONS; PHYLOGENY; PROTEIN SEQUENCES; PROTEIN STRUCTURES; RANDOMIZATION;

EID: 79954571926     PISSN: 03043975     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tcs.2010.10.040     Document Type: Article
Times cited : (8)

References (70)
  • 1
    • 0347314981 scopus 로고    scopus 로고
    • Physical complexity of symbolic sequences
    • C. Adami, and N.J. Cerf Physical complexity of symbolic sequences Physica D 137 2000 62 69
    • (2000) Physica D , vol.137 , pp. 62-69
    • Adami, C.1    Cerf, N.J.2
  • 2
    • 0032869219 scopus 로고    scopus 로고
    • Within- and between-species DNA sequence variation and the 'footprint' of natural selection
    • DOI 10.1016/S0378-1119(99)00294-2, PII S0378111999002942
    • H. Akashi Within- and between-species DNA sequence variation and the footprint of natural selection Gene 238 1999 39 51 (Pubitemid 29436096)
    • (1999) Gene , vol.238 , Issue.1 , pp. 39-51
    • Akashi, H.1
  • 4
    • 0034897709 scopus 로고    scopus 로고
    • The accuracy and power of likelihood ratio tests to detect positive selection at amino acid sites
    • M. Anisimova, J.P. Bielawski, and Z. Yang The accuracy and power of likelihood ratio tests to detect positive selection at amino acid sites Mol. Biol. Evol. 18 2001 1585 1592
    • (2001) Mol. Biol. Evol. , vol.18 , pp. 1585-1592
    • Anisimova, M.1    Bielawski, J.P.2    Yang, Z.3
  • 5
    • 0035896024 scopus 로고    scopus 로고
    • ConSurf: An algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information
    • DOI 10.1006/jmbi.2000.4474
    • A. Armon, D. Graur, and N. Ben-Tal ConSurf: an algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information J. Mol. Biol. 307 2001 447 463 (Pubitemid 33029992)
    • (2001) Journal of Molecular Biology , vol.307 , Issue.1 , pp. 447-463
    • Armon, A.1    Graur, D.2    Ben-Tal, N.3
  • 7
    • 55449127787 scopus 로고    scopus 로고
    • Predicting functional gene links from phylogenetic-statistical analyses of whole genomes
    • D. Barker, and M. Pagel Predicting functional gene links from phylogenetic-statistical analyses of whole genomes PLoS Comput. Biol. 1 1 2005 e3
    • (2005) PLoS Comput. Biol. , vol.1 , Issue.1 , pp. 3
    • Barker, D.1    Pagel, M.2
  • 8
    • 34247252941 scopus 로고    scopus 로고
    • Periodic distributions of hydrophobic amino acids allows the definition of fundamental building blocks to align distantly related proteins
    • DOI 10.1002/prot.21319
    • J. Baussand, C. Deremble, and A. Carbone Periodic distribution of hydrophobic amino acids allows the definition of fundamental building blocks to align distantly related proteins Proteins: Struct. Funct. Bioinf. 67 3 2007 695 708 (Pubitemid 46625585)
    • (2007) Proteins: Structure, Function and Genetics , vol.67 , Issue.3 , pp. 695-708
    • Baussand, J.1    Deremble, C.2    Carbone, A.3
  • 9
    • 70349656526 scopus 로고    scopus 로고
    • A combinatorial approach to detect co-evolved amino-acid networks in protein families with variable divergence
    • J. Baussand, and A. Carbone A combinatorial approach to detect co-evolved amino-acid networks in protein families with variable divergence PLoS Comput. Biol. 5 9 2009 e1000488
    • (2009) PLoS Comput. Biol. , vol.5 , Issue.9 , pp. 1000488
    • Baussand, J.1    Carbone, A.2
  • 10
    • 0035061474 scopus 로고    scopus 로고
    • Positive and negative selection in the DAZ gene family
    • J.P. Bielawski, and Z. Yang Positive and negative selection in the DAZ gene family Mol. Biol. Evol. 18 2001 523 529 (Pubitemid 32268004)
    • (2001) Molecular Biology and Evolution , vol.18 , Issue.4 , pp. 523-529
    • Bielawski, J.P.1    Yang, Z.2
  • 12
    • 79954595420 scopus 로고    scopus 로고
    • Information content of sets of biological sequences revisited
    • Algorithmic Bioprocesses
    • A. Carbone, and S. Engelen Information content of sets of biological sequences revisited A. Condon, D. Harel, J.N. Kok, A. Salomaa, E. Winfree, Algorithmic Bioprocesses Natural Computing Series 2008 Springer
    • (2008) Natural Computing Series
    • Carbone, A.1    Engelen, S.2
  • 14
    • 3342888069 scopus 로고    scopus 로고
    • Empirical analysis of protein insertions and deletions determining parameters for the correct placement of gaps in protein sequence alignments
    • DOI 10.1016/j.jmb.2004.05.045, PII S0022283604006151
    • M.S.S. Chang, and S.A. Benner Empirical analysis of protein insertions and deletions determining parameters for the correct placement of gaps in protein sequence alignments J. Mol. Biol. 341 2004 617 631 (Pubitemid 38987792)
    • (2004) Journal of Molecular Biology , vol.341 , Issue.2 , pp. 617-631
    • Chang, M.S.S.1    Benner, S.A.2
  • 15
    • 27144551715 scopus 로고    scopus 로고
    • Improvement in protein functional site prediction by distinguishing structural and functional constraints on protein family evolution using computational design
    • DOI 10.1093/nar/gki894
    • G. Cheng, B. Qian, R. Samudrala, and D. Baker Improvement in protein functional site prediction by distinguishing structural and functional constraints on protein family evolution using computational design Nucleic Acids Res. 33 2005 5861 5867 (Pubitemid 41742605)
    • (2005) Nucleic Acids Research , vol.33 , Issue.18 , pp. 5861-5867
    • Cheng, G.1    Qian, B.2    Samudrala, R.3    Baker, D.4
  • 16
    • 0033028201 scopus 로고    scopus 로고
    • Parallel evolution of drug resistance in HIV: Failure of nonsynonymous/synonymous substitution rate ratio to detect selection
    • K.A. Crandall, C.R. Kelsey, H. Imamichi, H.C. Lane, and N.P. Salzman Parallel evolution of drug resistance in HIV: failure of nonsynonymous/ synonymous substitution rate ratio to detect selection Mol. Biol. Evol. 16 1999 372 382 (Pubitemid 29119974)
    • (1999) Molecular Biology and Evolution , vol.16 , Issue.3 , pp. 372-382
    • Crandall, K.A.1    Kelsey, C.R.2    Imamichi, H.3    Lane, H.C.4    Salzman, N.P.5
  • 17
    • 3543089710 scopus 로고    scopus 로고
    • A perturbation-based method for calculating explicit likelihood of evolutionary co-variance in multiple sequence alignments
    • DOI 10.1093/bioinformatics/bth128
    • J.P. Dekker, A. Fodor, R.W. Aldrich, and G. Yellen A perturbation-based method for calculating explicit likelihood of evolutionary co-variance in multiple sequence alignments Bioinformatics 20 2004 1565 1572 (Pubitemid 39023160)
    • (2004) Bioinformatics , vol.20 , Issue.10 , pp. 1565-1572
    • Dekker, J.P.1    Fodor, A.2    Aldrich, R.W.3    Gary, Y.4
  • 18
    • 33745461893 scopus 로고    scopus 로고
    • Residues crucial for maintaining short paths in network communication mediate signaling in proteins
    • A. Del Sol, H. Fujihashi, D. Amoros, and R. Nussinov Residues crucial for maintaining short paths in network communication mediate signaling in proteins Mol. Syst. Biol. 2 2006 2006.0019
    • (2006) Mol. Syst. Biol. , vol.2 , pp. 20060019
    • Del Sol, A.1    Fujihashi, H.2    Amoros, D.3    Nussinov, R.4
  • 19
    • 34548815693 scopus 로고    scopus 로고
    • Modular architecture of protein structures and allosteric communications: Potential implications for signaling proteins and regulatory linkages
    • A. Del Sol, M.J. Arauzo-Bravo, D. Amoros, and R. Nussinov Modular architecture of protein structures and allosteric communications: potential implications for signaling proteins and regulatory linkages Genome Biol. 8 2006 R92
    • (2006) Genome Biol. , vol.8 , pp. 92
    • Del Sol, A.1    Arauzo-Bravo, M.J.2    Amoros, D.3    Nussinov, R.4
  • 20
    • 31344432159 scopus 로고    scopus 로고
    • Determination of network of residues that regulate allostery in protein families using sequence analysis
    • DOI 10.1110/ps.051767306
    • RI Dima, and D. Thirumalai Determination of networks of residues that regulate allostery in protein families using sequence analysis Protein Sci. 15 2006 258 268 (Pubitemid 43144998)
    • (2006) Protein Science , vol.15 , Issue.2 , pp. 258-268
    • Dima, R.I.1    Thirumalai, D.2
  • 21
    • 38849115223 scopus 로고    scopus 로고
    • Mutual information without the influence of phylogeny or entropy dramatically improves residue contact prediction
    • DOI 10.1093/bioinformatics/btm604
    • S.D. Dunn, L.M. Wahl, and G.B. Gloor Mutual information without the influence of phylogeny or entropy dramatically improves residue contact prediction Bioinformatics 24 2008 333 340 (Pubitemid 351189008)
    • (2008) Bioinformatics , vol.24 , Issue.3 , pp. 333-340
    • Dunn, S.D.1    Wahl, L.M.2    Gloor, G.B.3
  • 22
    • 0003234370 scopus 로고    scopus 로고
    • Multiple alignment for structural functional or phylogenetic analyses of homologous sequences
    • L. Duret, and S. Abdeddaim Multiple alignment for structural functional or phylogenetic analyses of homologous sequences D. Higgins, W. Taylor, Bioinformatics Sequence Structure and Databanks 2000 Oxford University Press Oxford
    • (2000) Bioinformatics Sequence Structure and Databanks
    • Duret, L.1    Abdeddaim, S.2
  • 23
    • 0030007094 scopus 로고    scopus 로고
    • Large-scale search for genes on which positive selection may operate
    • T. Endo, K. Ikeo, and T. Gojobori Large-scale search for genes on which positive selection may operate Mol. Biol. Evol. 13 1996 685 690 (Pubitemid 26131890)
    • (1996) Molecular Biology and Evolution , vol.13 , Issue.5 , pp. 685-690
    • Endo, T.1    Ikeo, K.2    Gojobori, T.3
  • 24
    • 59149089414 scopus 로고    scopus 로고
    • Joint Evolutionary Trees: Detection and analysis of protein interfaces
    • 101371/journalpcbi1000267
    • S. Engelen, L.A. Trojan, S. Sacquin-Mora, R. Lavery, and A. Carbone Joint Evolutionary Trees: detection and analysis of protein interfaces PLoS Comput. Biol. 5 1 2009 e1000267 10.1371/journal.pcbi.1000267
    • (2009) PLoS Comput. Biol. , vol.5 , Issue.1 , pp. 1000267
    • Engelen, S.1    Trojan, L.A.2    Sacquin-Mora, S.3    Lavery, R.4    Carbone, A.5
  • 25
    • 0035157361 scopus 로고    scopus 로고
    • Evidence for positive selection in the capsid protein-coding region of the foot-and-mouth disease virus (FMDV) subjected to experimental passage regimens
    • M.A. Fares, A. Moya, C. Escarmis, E. Baranowski, E. Domingo, and E. Barrio Evidence for positive selection in the capsid protein-coding region of the foot-and-mouth disease virus (FMDV) subjected to experimental passage regimens Mol. Biol. Evol. 18 2001 10 21 (Pubitemid 32063969)
    • (2001) Molecular Biology and Evolution , vol.18 , Issue.1 , pp. 10-21
    • Fares, M.A.1    Moya, A.2    Escarmis, C.3    Baranowski, E.4    Domingo, E.5    Barrio, E.6
  • 26
    • 33744457709 scopus 로고    scopus 로고
    • A novel method for detecting intramolecular coevolution: Adding a further dimension to selective constraints analyses
    • DOI 10.1534/genetics.105.053249
    • M.A. Fares, and S.A.A. Travers A novel method for detecting intramolecular coevolution: adding a further dimension to selective constraints analyses Genetics 173 2006 9 23 (Pubitemid 43800180)
    • (2006) Genetics , vol.173 , Issue.1 , pp. 9-23
    • Fares, M.A.1    Travers, S.A.A.2
  • 28
    • 0014860857 scopus 로고
    • An improved method for determining codon variability in a gene and its application to the rate of fixation of mutations in evolution
    • W.M. Fitch, and E. Markowitz An improved method for determining codon variability in a gene and its application to the rate of fixation of mutations in evolution Biochem. Genet. 4 1970 579 593
    • (1970) Biochem. Genet. , vol.4 , pp. 579-593
    • Fitch, W.M.1    Markowitz, E.2
  • 29
    • 3042842115 scopus 로고    scopus 로고
    • Influence of conservation on calculations of amino acid covariance in multiple sequence alignments
    • DOI 10.1002/prot.20098
    • A.A. Fodor, and R.W. Aldrich Influence of conservation on calculations of amino acid covariance in multiple sequence alignments Proteins 56 2004 211 221 (Pubitemid 38850156)
    • (2004) Proteins: Structure, Function and Genetics , vol.56 , Issue.2 , pp. 211-221
    • Fodor, A.A.1    Aldrich, R.W.2
  • 30
    • 0035057075 scopus 로고    scopus 로고
    • Molecular evolution of transferrin: Evidence for positive selection in salmonids
    • M.J. Ford Molecular evolution of transferrin: evidence for positive selection in salmonids Mol. Biol. Evol. 18 2001 639 647 (Pubitemid 32268017)
    • (2001) Molecular Biology and Evolution , vol.18 , Issue.4 , pp. 639-647
    • Ford, M.J.1
  • 31
    • 18544362952 scopus 로고    scopus 로고
    • Mutual information in protein multiple sequence alignments reveals two classes of coevolving positions
    • DOI 10.1021/bi050293e
    • G.B. Gloor, L.C. Martin, L.N. Wahl, and S.D. Dunn Mutual information in protein multiple sequence alignments reveals two two classes of coevolving positions Biochemistry 44 2005 7156 7165 (Pubitemid 40656660)
    • (2005) Biochemistry , vol.44 , Issue.19 , pp. 7156-7165
    • Gloor, G.B.1    Martin, L.C.2    Wahl, L.M.3    Dunn, S.D.4
  • 33
    • 0028168856 scopus 로고
    • A codon-based model of nucleotide substitution for protein-coding DNA sequences
    • N. Goldman, and Z. Yang A codon-based model of nucleotide substitution for protein-coding DNA sequences Mol. Biol. Evol. 11 1994 725 736
    • (1994) Mol. Biol. Evol. , vol.11 , pp. 725-736
    • Goldman, N.1    Yang, Z.2
  • 34
    • 0035148533 scopus 로고    scopus 로고
    • Evidence for positive selection in foot-and-mouth disease virus capsid genes from field isolates
    • D.T. Haydon, A.D. Bastos, N.J. Knowles, and A.R. Samuel Evidence for positive selection in foot-and-mouth-disease virus capsid genes from field isolates Genetics 157 2001 7 15 (Pubitemid 32066292)
    • (2001) Genetics , vol.157 , Issue.1 , pp. 7-15
    • Haydon, D.T.1    Bastos, A.D.2    Knowles, N.J.3    Samuel, A.R.4
  • 35
    • 0023764283 scopus 로고
    • Pattern of nucleotide substitution at major histocompatibility complex class i loci reveals overdominant selection
    • A.L. Hughes, and M. Nei Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection Nature 335 1988 167 170
    • (1988) Nature , vol.335 , pp. 167-170
    • Hughes, A.L.1    Nei, M.2
  • 37
    • 34547600100 scopus 로고    scopus 로고
    • SiteFiNDER-3D: A web-based tool for predicting the location of functional sites in proteins
    • C.A. Innis siteFiNDER-3D: a web-based tool for predicting the location of functional sites in proteins Nucleic Acids Res. 35 Web-Server-Issue 2007 489 494
    • (2007) Nucleic Acids Res. , vol.35 , Issue.WEB-SERVER-ISSUE , pp. 489-494
    • Innis, C.A.1
  • 38
    • 0036721218 scopus 로고    scopus 로고
    • Mapping pathways of allosteric communication in GroEL by analysis of correlated mutations
    • DOI 10.1002/prot.10180
    • I. Kass, and A. Horovitz Mapping pathways of allosteric communication in GroEL by analysis of correlated mutations Proteins: Struct. Funct. Bioinf. 48 2002 611 617 (Pubitemid 34925449)
    • (2002) Proteins: Structure, Function and Genetics , vol.48 , Issue.4 , pp. 611-617
    • Kass, I.1    Horovitz, A.2
  • 39
    • 0035972742 scopus 로고    scopus 로고
    • Multiple alignment of complete sequences (MACS) in the post-genomic era
    • DOI 10.1016/S0378-1119(01)00461-9, PII S0378111901004619
    • O. Lecompte, J.D. Thompson, F. Plewniak, J. Thierry, and O. Poch Multiple alignment of complete sequences (MACS) in the post-genomic era Gene 270 2001 17 30 (Pubitemid 32525798)
    • (2001) Gene , vol.270 , Issue.1-2 , pp. 17-30
    • Lecompte, O.1    Thompson, J.D.2    Plewniak, F.3    Thierry, J.-C.4    Poch, O.5
  • 40
    • 0029913807 scopus 로고    scopus 로고
    • An evolutionary trace method defines binding surfaces common to protein families
    • DOI 10.1006/jmbi.1996.0167
    • O. Lichtarge, H.R. Bourne, and F.E. Cohen An evolutionary trace method defines binding surfaces common to protein families J. Mol. Biol. 257 1996 342 358 (Pubitemid 26114038)
    • (1996) Journal of Molecular Biology , vol.257 , Issue.2 , pp. 342-358
    • Lichtarge, O.1    Bourne, H.R.2    Cohen, F.E.3
  • 41
    • 0036468670 scopus 로고    scopus 로고
    • Evolutionary predictions of binding surfaces and interactions
    • DOI 10.1016/S0959-440X(02)00284-1
    • O. Lichtarge, and M.E. Sowa Evolutionary predictions of binding surfaces and interactions Curr. Opin. Struct. Biol. 12 2002 21 27 (Pubitemid 34142716)
    • (2002) Current Opinion in Structural Biology , vol.12 , Issue.1 , pp. 21-27
    • Lichtarge, O.1    Sowa, M.E.2
  • 42
    • 0033536602 scopus 로고    scopus 로고
    • Evolutionarily conserved pathways of energetic connectivity in protein families
    • DOI 10.1126/science.286.5438.295
    • S.W. Lockless, and R. Ranganathan Evolutionary conserved pathways of energetic connectivity in protein families Science 286 1999 295 299 (Pubitemid 29484693)
    • (1999) Science , vol.286 , Issue.5438 , pp. 295-299
    • Lockless, S.W.1    Ranganathan, R.2
  • 43
    • 27944458910 scopus 로고    scopus 로고
    • Using information theory to search for co-evolving residues in proteins
    • DOI 10.1093/bioinformatics/bti671
    • L.C. Martin, G.B. Gloor, S.D. Dunn, and L.M. Wahl Using information theory to search for co-evolving residues in proteins Bioinformatics 21 2005 4116 4124 (Pubitemid 41672101)
    • (2005) Bioinformatics , vol.21 , Issue.22 , pp. 4116-4124
    • Martin, L.C.1    Gloor, G.B.2    Dunn, S.D.3    Wahl, L.M.4
  • 44
    • 0028024626 scopus 로고
    • A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome
    • S.V. Muse, and B.S. Gaut A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome Mol. Biol. Evol. 11 1994 715 724 (Pubitemid 24274880)
    • (1994) Molecular Biology and Evolution , vol.11 , Issue.5 , pp. 715-724
    • Muse, S.V.1    Gaut, B.S.2
  • 45
    • 0030984551 scopus 로고    scopus 로고
    • Comparing patterns of nucleotide substitution rates among chloroplast loci using the relative ratio test
    • S.V. Muse, and B.S. Gaut Comparing patterns of nucleotide substitution rates among chloroplast loci using the relative ratio test Genetics 146 1997 393 399 (Pubitemid 27194416)
    • (1997) Genetics , vol.146 , Issue.1 , pp. 393-399
    • Muse, S.V.1    Gaut, B.S.2
  • 46
    • 0031972161 scopus 로고    scopus 로고
    • Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene
    • R. Nielsen, and Z. Yang Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene Genetics 148 1998 929 936 (Pubitemid 28169008)
    • (1998) Genetics , vol.148 , Issue.3 , pp. 929-936
    • Nielsen, R.1    Yang, Z.2
  • 47
    • 0036208872 scopus 로고    scopus 로고
    • Recent progress in multiple sequence alignment: A survey
    • DOI 10.1517/14622416.3.1.131
    • C. Notredame Recent progresses in multiple sequence alignment: a survey Pharmacogenomics 31 2002 131 144 (Pubitemid 34285245)
    • (2002) Pharmacogenomics , vol.3 , Issue.1 , pp. 131-144
    • Notredame, C.1
  • 48
    • 34548400364 scopus 로고    scopus 로고
    • Recent evolutions of multiple sequence alignment algorithms
    • C. Notredame Recent evolutions of multiple sequence alignment algorithms PLOS Comput. Biol. 8 2007 e123
    • (2007) PLOS Comput. Biol. , vol.8 , pp. 123
    • Notredame, C.1
  • 49
    • 22444450449 scopus 로고    scopus 로고
    • Intramolecular signaling pathways revealed by modeling anisotropic thermal diffusion
    • DOI 10.1016/j.jmb.2005.05.043, PII S002228360500598X
    • N. Ota, and D.A. Agard Intramolecular signaling pathways revealed by modeling anisotropic thermal diffusion Eur. J. Mol. Biol. 351 2005 345 354 (Pubitemid 41007753)
    • (2005) Journal of Molecular Biology , vol.351 , Issue.2 , pp. 345-354
    • Ota, N.1    Agard, D.A.2
  • 50
    • 0035095812 scopus 로고    scopus 로고
    • The interaction of protein structure, selection, and recombination on the evolution of the type-1 fimbrial major subunit (fimA) from Escherichia coli
    • A.S. Peek, V. Souza, L.E. Eguiarte, and B.S. Gaut The interaction of protein structure, selection, and recombination on the evolution of the type-1 fimbrial major subunit (fimA) from Escherichia coli J. Mol. Evol. 52 2001 193 204 (Pubitemid 32260635)
    • (2001) Journal of Molecular Evolution , vol.52 , Issue.2 , pp. 193-204
    • Peek, A.S.1    Souza, V.2    Eguiarte, L.E.3    Gaut, B.S.4
  • 51
    • 0030743758 scopus 로고    scopus 로고
    • Effectiveness of correlation analysis in identifying protein residues undergoing correlated evolution
    • D.D. Pollock, and W.R. Taylor Effectiveness of correlation analysis in identifying protein residues undergoing correlated evolution Protein Eng. 10 1997 647 657 (Pubitemid 27332071)
    • (1997) Protein Engineering , vol.10 , Issue.6 , pp. 647-657
    • Pollock, D.D.1    Taylor, W.R.2
  • 52
    • 21044438202 scopus 로고    scopus 로고
    • The rate of compensatory mutation in the DNA bacteriophage φX174
    • DOI 10.1534/genetics.104.039438
    • A. Poon, and L. Chao The rate of compensatory mutation in the DNA bacteriophage X174 Genetics 170 2005 989 999 (Pubitemid 41105458)
    • (2005) Genetics , vol.170 , Issue.3 , pp. 989-999
    • Poon, A.1    Chao, L.2
  • 53
    • 0002218484 scopus 로고    scopus 로고
    • Rate4Site: An algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues
    • T. Pupko, R.E. Bell, I. Mayrose, F. Glaser, and N. Ben-Tal Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues Bioinformatics 18 2002 S71 S77
    • (2002) Bioinformatics , vol.18
    • Pupko, T.1    Bell, R.E.2    Mayrose, I.3    Glaser, F.4    Ben-Tal, N.5
  • 54
    • 0037436412 scopus 로고    scopus 로고
    • Exploiting the co-evolution of interacting proteins to discover interaction specificity
    • DOI 10.1016/S0022-2836(03)00114-1
    • A.K. Ramani, and E.M. Marcotte Exploiting the coevolution of interacting proteins to discover interaction specificity J. Mol. Biol. 327 2003 273 284 (Pubitemid 36293318)
    • (2003) Journal of Molecular Biology , vol.327 , Issue.1 , pp. 273-284
    • Ramani, A.K.1    Marcotte, E.M.2
  • 55
    • 0030928378 scopus 로고    scopus 로고
    • Seq-gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees
    • A. Rambaut, and N.C. Grassly Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees Comput. Appl. Biosci. 13 1997 235 238 (Pubitemid 27249927)
    • (1997) Computer Applications in the Biosciences , vol.13 , Issue.3 , pp. 235-238
    • Rambaut, A.1    Grassly, N.C.2
  • 56
    • 1842328059 scopus 로고    scopus 로고
    • In search of molecular Darwinism
    • P.M. Sharp In search of molecular Darwinism Nature 385 1997 111 112
    • (1997) Nature , vol.385 , pp. 111-112
    • Sharp, P.M.1
  • 57
    • 33847668252 scopus 로고    scopus 로고
    • Indel-Seq-Gen: A new protein family simulator incorporating domains, motifs, and indels
    • DOI 10.1093/molbev/msl195
    • C.L. Strope, S.D. Scott, and E.N. Moriyama indel-Seq-Gen: a new protein family simulator incorporating domains, motifs, and indels Mol. Biol. Evol. 24 2007 640 649 (Pubitemid 46355791)
    • (2007) Molecular Biology and Evolution , vol.24 , Issue.3 , pp. 640-649
    • Strope, C.L.1    Scott, S.D.2    Moriyama, E.N.3
  • 58
    • 0037219686 scopus 로고    scopus 로고
    • Evolutionarily conserved networks of residues mediate allosteric communication in proteins
    • DOI 10.1038/nsb881
    • G.M. Suel, S.W. Lockless, M.A. Wall, and R. Ranganathan Evolutionary conserved networks of residues mediate allosteric communication in proteins Nature Struct. Biol. 23 2003 59 69 (Pubitemid 36034178)
    • (2003) Nature Structural Biology , vol.10 , Issue.1 , pp. 59-69
    • Suel, G.M.1    Lockless, S.W.2    Wall, M.A.3    Ranganathan, R.4
  • 60
    • 0033168097 scopus 로고    scopus 로고
    • A comprehensive comparison of multiple sequence alignment programs
    • J.D. Thompson, F. Plewniak, and O. Poch A comprehensive comparison of multiple sequence alignment programs Nucleic Acids Res. 27 1999 12682 12690
    • (1999) Nucleic Acids Res. , vol.27 , pp. 12682-12690
    • Thompson, J.D.1    Plewniak, F.2    Poch, O.3
  • 61
    • 0037433701 scopus 로고    scopus 로고
    • Using multiple interdependency to separate functional from phylogenetic correlations in protein alignments
    • DOI 10.1093/bioinformatics/btg072
    • E.R. Tillier, and T.W. Lui Using multiple interdependency to separate functional from phylogenetic correlations in protein alignments Bioinformatics 19 2003 750 755 (Pubitemid 36511899)
    • (2003) Bioinformatics , vol.19 , Issue.6 , pp. 750-755
    • Tillier, E.R.M.1    Lui, T.W.H.2
  • 63
    • 0033639150 scopus 로고    scopus 로고
    • Statistical methods for detecting molecular adaptation
    • Z. Yang, and J.P. Bielawski Statistical methods for detecting molecular adaptation Trends Ecol. Evol. 15 2000 496 503
    • (2000) Trends Ecol. Evol. , vol.15 , pp. 496-503
    • Yang, Z.1    Bielawski, J.P.2
  • 64
    • 0034097381 scopus 로고    scopus 로고
    • Codon-substitution models for heterogeneous selection pressure at amino acid sites
    • Z. Yang, R. Nielsen, N. Goldman, and AMK Pedersen Codon-substitution models for heterogeneous selection pressure at amino acid sites Genetics 155 2000 431 449 (Pubitemid 30257141)
    • (2000) Genetics , vol.155 , Issue.1 , pp. 431-449
    • Yang, Z.1    Nielsen, R.2    Goldman, N.3    Pedersen, A.-M.K.4
  • 65
    • 6644223187 scopus 로고
    • Protein structure relationships revealed by mutational analysis
    • C. Yanofsky, V. Horn, and D. Thorpe Protein structure relationships revealed by mutational analysis Science 146 1964 1593 1594
    • (1964) Science , vol.146 , pp. 1593-1594
    • Yanofsky, C.1    Horn, V.2    Thorpe, D.3
  • 66
    • 36949019322 scopus 로고    scopus 로고
    • Detecting coevolution in and among proteins domains
    • C.-H. Yeang, and D. Haussler Detecting coevolution in and among proteins domains PLoS Comput. Biol. 3 2007 2122 2134
    • (2007) PLoS Comput. Biol. , vol.3 , pp. 2122-2134
    • Yeang, C.-H.1    Haussler, D.2
  • 68
    • 20444450051 scopus 로고    scopus 로고
    • Predicting protein function from sequence and structural data
    • DOI 10.1016/j.sbi.2005.04.003, PII S0959440X05000825
    • J.D. Watson, R.A. Laskowski, and J.M. Thornton Predicting protein function from sequence and structural data Curr. Opin. Struct. Biol. 15 2005 275 284 (Pubitemid 40826446)
    • (2005) Current Opinion in Structural Biology , vol.15 , Issue.SPEC. ISS. 3 , pp. 275-284
    • Watson, J.D.1    Laskowski, R.A.2    Thornton, J.M.3
  • 70
    • 0032737463 scopus 로고    scopus 로고
    • Genealogical evidence for positive selection in the nef gene of HIV-1
    • P.M. Zanotto, E.G. Kallas, R.F. Souza, and E.C. Holmes Genealogical evidence for positive selection in the nef gene of HIV-1 Genetics 153 1999 1077 1089 (Pubitemid 29522126)
    • (1999) Genetics , vol.153 , Issue.3 , pp. 1077-1089
    • Zanotto, P.M.D.A.1    Kallas, E.G.2    De Souza, R.F.3    Holmes, E.C.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.