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Volumn 33, Issue 4, 1998, Pages 518-534

Patterns of protein-fold usage in eight microbial genomes: A comprehensive structural census

Author keywords

Protein structure; Structure databank; Superfold

Indexed keywords

ARTICLE; BACTERIAL GENETICS; CYANOBACTERIUM; ESCHERICHIA COLI; GENE EXPRESSION; GENOME; HAEMOPHILUS INFLUENZAE; HELICOBACTER PYLORI; MYCOPLASMA GENITALIUM; MYCOPLASMA PNEUMONIAE; NONHUMAN; PRIORITY JOURNAL; PROTEIN FOLDING; YEAST;

EID: 0032387685     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(19981201)33:4<518::AID-PROT5>3.0.CO;2-J     Document Type: Article
Times cited : (103)

References (128)
  • 1
    • 0029059785 scopus 로고
    • Bacterial genome sequence bagged
    • Nowak, R. Bacterial genome sequence bagged. Science 269:468-470, 1995.
    • (1995) Science , vol.269 , pp. 468-470
    • Nowak, R.1
  • 2
    • 0345462856 scopus 로고    scopus 로고
    • Scientists unlock sequence of ulcer bacterium's genes
    • August 7
    • Langreth, R. Scientists unlock sequence of ulcer bacterium's genes. Wall Street Journal B1, August 7, 1997.
    • (1997) Wall Street Journal , vol.B1
    • Langreth, R.1
  • 3
    • 0010702328 scopus 로고    scopus 로고
    • Thinking small paying off big in gene quest
    • 3 February
    • Wade, N. Thinking small paying off big in gene quest. New York Times, 3 February 1997, A1.
    • (1997) New York Times
    • Wade, N.1
  • 5
    • 0029060923 scopus 로고
    • Dinucleotide relative abundance extremes: A genomic signature
    • Karlin, S., Burge, C. Dinucleotide relative abundance extremes: a genomic signature [Review]. Trends Genet. 11:283-290, 1995.
    • (1995) Trends Genet. , vol.11 , pp. 283-290
    • Karlin, S.1    Burge, C.2
  • 6
    • 0026600016 scopus 로고
    • Statistical analyses of counts and distributions of restriction sites in DNA sequences
    • Karlin, S., Burge, C., Campbell, A.M. Statistical analyses of counts and distributions of restriction sites in DNA sequences. Nucleic Acids Res. 20:1363-1370, 1992.
    • (1992) Nucleic Acids Res. , vol.20 , pp. 1363-1370
    • Karlin, S.1    Burge, C.2    Campbell, A.M.3
  • 7
    • 10344260141 scopus 로고    scopus 로고
    • Frequent oligo-nucleotides and peptides of the Haemophilus influenzae genome
    • Karlin, S., Mrazek, J., Campbell, A.M. Frequent oligo-nucleotides and peptides of the Haemophilus influenzae genome. Nucleic Acids Res. 24:4263-4272, 1996.
    • (1996) Nucleic Acids Res. , vol.24 , pp. 4263-4272
    • Karlin, S.1    Mrazek, J.2    Campbell, A.M.3
  • 8
    • 0030113436 scopus 로고    scopus 로고
    • Sequencing and analysis of bacterial genomes
    • Koonin, E.V., Mushegian, A.R., Rudd, K.E. Sequencing and analysis of bacterial genomes. Curr Biol. 6:404-416, 1996.
    • (1996) Curr Biol. , vol.6 , pp. 404-416
    • Koonin, E.V.1    Mushegian, A.R.2    Rudd, K.E.3
  • 10
    • 0030860218 scopus 로고    scopus 로고
    • Genes and proteins of Escherichia coli K-12 (GenProtEC)
    • Riley, M. Genes and proteins of Escherichia coli K-12 (GenProtEC). Nucleic Acids Res 25:51-52, 1997.
    • (1997) Nucleic Acids Res , vol.25 , pp. 51-52
    • Riley, M.1
  • 11
    • 0030947344 scopus 로고    scopus 로고
    • Molecular evidence for an ancient duplication of the entire yeast genome
    • Wolfe, K.H., Shields, D.C. Molecular evidence for an ancient duplication of the entire yeast genome. Nature 387:708-713, 1997.
    • (1997) Nature , vol.387 , pp. 708-713
    • Wolfe, K.H.1    Shields, D.C.2
  • 12
    • 0031565915 scopus 로고    scopus 로고
    • A structural census of genomes: Comparing eukaryotic, bacterial and archaeal genomes in terms of protein structure
    • Gerstein M. A structural census of genomes: comparing eukaryotic, bacterial and archaeal genomes in terms of protein structure. J. Mol. Biol. 274:562-576, 1997.
    • (1997) J. Mol. Biol. , vol.274 , pp. 562-576
    • Gerstein, M.1
  • 13
    • 0031024670 scopus 로고    scopus 로고
    • Conserved clusters of functionally related genes in two bacterial genomes
    • Tamames, J., Casari, G., Ouzounis, C., Valencia, A. Conserved clusters of functionally related genes in two bacterial genomes. J. Mol. Evol. 44:66-73, 1997.
    • (1997) J. Mol. Evol. , vol.44 , pp. 66-73
    • Tamames, J.1    Casari, G.2    Ouzounis, C.3    Valencia, A.4
  • 14
    • 0027399170 scopus 로고
    • Ancient conserved regions in new gene sequences and the protein databases
    • Green, P., Lipman, D., Hillier, L., Waterston, R., States, D., Claverie, J.M. Ancient conserved regions in new gene sequences and the protein databases. Science 259:1711-1716, 1993.
    • (1993) Science , vol.259 , pp. 1711-1716
    • Green, P.1    Lipman, D.2    Hillier, L.3    Waterston, R.4    States, D.5    Claverie, J.M.6
  • 15
    • 0029559311 scopus 로고
    • Sequence similarity analysis of Escherichia coli proteins: Functional and evolutionary implications
    • Koonin, E.V., Tatusov, R.L., Rudd, K.E. Sequence similarity analysis of Escherichia coli proteins: functional and evolutionary implications. Proc. Natl. Acad. Sci. USA 92:11921-11925, 1995.
    • (1995) Proc. Natl. Acad. Sci. USA , vol.92 , pp. 11921-11925
    • Koonin, E.V.1    Tatusov, R.L.2    Rudd, K.E.3
  • 16
    • 0030660581 scopus 로고    scopus 로고
    • A genomic perspective on protein families
    • Tatusov, R.L., Koonin, E.V., Lipman, D.J. A genomic perspective on protein families. Science 278:631-637, 1997.
    • (1997) Science , vol.278 , pp. 631-637
    • Tatusov, R.L.1    Koonin, E.V.2    Lipman, D.J.3
  • 18
    • 0028882241 scopus 로고
    • New protein functions in yeast chromosome VIII
    • Ouzounis, C., Bork, P., Casari, G., Sander, C. New protein functions in yeast chromosome VIII. Protein Sci. 4:2424-2428, 1995.
    • (1995) Protein Sci. , vol.4 , pp. 2424-2428
    • Ouzounis, C.1    Bork, P.2    Casari, G.3    Sander, C.4
  • 19
    • 0031000180 scopus 로고    scopus 로고
    • The first genome from the third domain of life
    • Clayton, R.A., White, O., Ketchum, K.A., Venter, J.C. The first genome from the third domain of life [news]. Nature 387:459-462, 1997.
    • (1997) Nature , vol.387 , pp. 459-462
    • Clayton, R.A.1    White, O.2    Ketchum, K.A.3    Venter, J.C.4
  • 20
    • 0029867572 scopus 로고    scopus 로고
    • EcoCyc: Electronic encyclopedia of E. coli genes and metabolism
    • Karp, P., Riley, M., Paley, S., Pellegrini-Toole, A. EcoCyc: electronic encyclopedia of E. coli genes and metabolism. Nucleic Acids Res. 24:32-40, 1996.
    • (1996) Nucleic Acids Res. , vol.24 , pp. 32-40
    • Karp, P.1    Riley, M.2    Paley, S.3    Pellegrini-Toole, A.4
  • 22
    • 0029789824 scopus 로고    scopus 로고
    • A minimal gene set for cellular life derived by comparison of complete bacterial genomes
    • Mushegian, A.R., Koonin, E.V. A minimal gene set for cellular life derived by comparison of complete bacterial genomes [see comments]. Proc. Natl. Acad. Sci. USA 93:10268-10273, 1996.
    • (1996) Proc. Natl. Acad. Sci. USA , vol.93 , pp. 10268-10273
    • Mushegian, A.R.1    Koonin, E.V.2
  • 23
    • 0030111235 scopus 로고    scopus 로고
    • Metabolism and evolution of Haemophilus influenzae deduced from a whole-genome comparison with Escherichia coli
    • Tatusov, R.L., Mushegian, A.R., Bork, P., et al. Metabolism and evolution of Haemophilus influenzae deduced from a whole-genome comparison with Escherichia coli. Curr. Biol. 6:279-291, 1996.
    • (1996) Curr. Biol. , vol.6 , pp. 279-291
    • Tatusov, R.L.1    Mushegian, A.R.2    Bork, P.3
  • 24
    • 0029653518 scopus 로고
    • Whole-genome random sequencing and assembly of Haemophilus influenzae rd
    • Fleischmann, R.D., Adams, M.D., White, O., et al. Whole-genome random sequencing and assembly of Haemophilus influenzae rd. Science 269:496-512, 1995.
    • (1995) Science , vol.269 , pp. 496-512
    • Fleischmann, R.D.1    Adams, M.D.2    White, O.3
  • 26
    • 0027057935 scopus 로고
    • Comprehensive sequence analysis of the 182 predicted open reading frames of yeast chromosome iii
    • Bork, P., Ouzounis, C., Sander, C., Scharf, M., Schneider, R., Sonnhammer, E. Comprehensive sequence analysis of the 182 predicted open reading frames of yeast chromosome iii. Protein Sci. 1:1677-1690, 1992.
    • (1992) Protein Sci. , vol.1 , pp. 1677-1690
    • Bork, P.1    Ouzounis, C.2    Sander, C.3    Scharf, M.4    Schneider, R.5    Sonnhammer, E.6
  • 28
    • 0029144085 scopus 로고
    • Challenging times for bioinformatics
    • Casari, G., Andrade, M., Bork, P., et al. Challenging times for bioinformatics. Nature 376:647-648, 1995.
    • (1995) Nature , vol.376 , pp. 647-648
    • Casari, G.1    Andrade, M.2    Bork, P.3
  • 29
    • 0029828166 scopus 로고    scopus 로고
    • Fully automated genome analysis that reflects user needs and preferences. A detailed introduction to the MAGPIE system architecture
    • Gaasterland, T., Sensen, C.W. Fully automated genome analysis that reflects user needs and preferences. A detailed introduction to the MAGPIE system architecture. Biochimie 78:302-310, 1996.
    • (1996) Biochimie , vol.78 , pp. 302-310
    • Gaasterland, T.1    Sensen, C.W.2
  • 30
    • 0029091249 scopus 로고
    • Average core structures and variability measures for protein families: Application to the immunoglobulins
    • Gerstein, M., Altman, R. Average core structures and variability measures for protein families: application to the immunoglobulins. J. Mol. Biol. 251:161-175, 1995.
    • (1995) J. Mol. Biol. , vol.251 , pp. 161-175
    • Gerstein, M.1    Altman, R.2
  • 31
    • 0029565638 scopus 로고
    • A structurally invariant core for the globins
    • Gerstein, M., Altman, R. A structurally invariant core for the globins. CABIOS 11:633-644, 1995.
    • (1995) CABIOS , vol.11 , pp. 633-644
    • Gerstein, M.1    Altman, R.2
  • 32
    • 0026410103 scopus 로고
    • Automated assembly of protein blocks for database searching
    • Henikoff, S., Henikoff, J.G. Automated assembly of protein blocks for database searching. Proc. Natl. Acad. Sci. USA 19:6565-6572, 1993.
    • (1993) Proc. Natl. Acad. Sci. USA , vol.19 , pp. 6565-6572
    • Henikoff, S.1    Henikoff, J.G.2
  • 33
    • 0028118434 scopus 로고
    • Protein family classification based on searching a database of blocks
    • Henikoff, S., Henikoff, J.G. Protein family classification based on searching a database of blocks. Genomics 19:97-107, 1994.
    • (1994) Genomics , vol.19 , pp. 97-107
    • Henikoff, S.1    Henikoff, J.G.2
  • 35
    • 0028218683 scopus 로고
    • Modular arrangement of proteins as inferred from analysis of homology
    • Sonnhammer, E.L.L., Kahn, D. Modular arrangement of proteins as inferred from analysis of homology. Protein Sci. 3:482-492, 1994.
    • (1994) Protein Sci. , vol.3 , pp. 482-492
    • Sonnhammer, E.L.L.1    Kahn, D.2
  • 36
    • 0030925920 scopus 로고    scopus 로고
    • Pfam: A comprehensive database of protein domain families based on seed alignments
    • Sonnhammer, E., Eddy, S., Durbin, R. Pfam: a comprehensive database of protein domain families based on seed alignments. Proteins 28:405-420, 1997.
    • (1997) Proteins , vol.28 , pp. 405-420
    • Sonnhammer, E.1    Eddy, S.2    Durbin, R.3
  • 37
    • 0031584266 scopus 로고    scopus 로고
    • Protein evolution viewed through Escherichia coli protein sequences: Introducing the notion of a structural segment of homology, the module
    • Riley, M., Labedan, B. Protein evolution viewed through Escherichia coli protein sequences: introducing the notion of a structural segment of homology, the module. J. Mol. Biol. 268:857-868, 1997.
    • (1997) J. Mol. Biol. , vol.268 , pp. 857-868
    • Riley, M.1    Labedan, B.2
  • 38
    • 1842377444 scopus 로고    scopus 로고
    • The SBASE protein domain library, release 5.0: A collection of annotated protein sequence segments
    • Fabian, P., Murvai, J., Hatsagi, Z., Vlahovicek, K., Hegyi, H., Pongor, S. The SBASE protein domain library, release 5.0: a collection of annotated protein sequence segments. Nucleic Acids Res. 25:240-243, 1997.
    • (1997) Nucleic Acids Res. , vol.25 , pp. 240-243
    • Fabian, P.1    Murvai, J.2    Hatsagi, Z.3    Vlahovicek, K.4    Hegyi, H.5    Pongor, S.6
  • 39
    • 0022706389 scopus 로고
    • The relation between the divergence of sequence and structure in proteins
    • Chothia, C., Lesk, A.M. The relation between the divergence of sequence and structure in proteins. EMBO J. 5:823-826, 1986.
    • (1986) EMBO J. , vol.5 , pp. 823-826
    • Chothia, C.1    Lesk, A.M.2
  • 40
    • 0031020765 scopus 로고    scopus 로고
    • Protein evolution. How far can sequences diverge?
    • Chothia, C., Gerstein, M. Protein evolution. How far can sequences diverge? Nature 385:579-581, 1997.
    • (1997) Nature , vol.385 , pp. 579-581
    • Chothia, C.1    Gerstein, M.2
  • 41
    • 0027122748 scopus 로고
    • Proteins - 1000 families for the molecular biologist
    • Chothia, C. Proteins - 1000 families for the molecular biologist. Nature 357:543-544, 1992.
    • (1992) Nature , vol.357 , pp. 543-544
    • Chothia, C.1
  • 42
    • 0029805706 scopus 로고    scopus 로고
    • The genomics: Global views of biology
    • Lander, E.S. The genomics: global views of biology. Science 274:536-539, 1996.
    • (1996) Science , vol.274 , pp. 536-539
    • Lander, E.S.1
  • 43
    • 0022797368 scopus 로고
    • Alignment of amino acid sequences of distantly related proteins using variable gap penalties
    • Lesk, A.M., Levitt, M., Chothia, C. Alignment of amino acid sequences of distantly related proteins using variable gap penalties. Protein Eng. 1:77-78, 1986.
    • (1986) Protein Eng. , vol.1 , pp. 77-78
    • Lesk, A.M.1    Levitt, M.2    Chothia, C.3
  • 45
    • 0030720480 scopus 로고    scopus 로고
    • A structural census of the current population of protein sequences
    • Gerstein, M., Levitt, M. A structural census of the current population of protein sequences. Proc. Natl. Acad. Sci. USA 94:11911-11916, 1997.
    • (1997) Proc. Natl. Acad. Sci. USA , vol.94 , pp. 11911-11916
    • Gerstein, M.1    Levitt, M.2
  • 46
    • 0030724017 scopus 로고    scopus 로고
    • Assigning folds to the proteins encoded by the genome of Mycoplasma genitalium
    • Fischer, D., Eisenberg, D. Assigning folds to the proteins encoded by the genome of Mycoplasma genitalium [In Process Citation]. Proc. Natl. Acad. Sci. USA 94:11929-11934, 1997.
    • (1997) Proc. Natl. Acad. Sci. USA , vol.94 , pp. 11929-11934
    • Fischer, D.1    Eisenberg, D.2
  • 47
    • 0027183678 scopus 로고
    • How many yeast genes code for membrane-spanning proteins?
    • Goffeau, A., Slonimski, P., Nakai, K., Risler, J.L. How many yeast genes code for membrane-spanning proteins? Yeast 9:691-702, 1993.
    • (1993) Yeast , vol.9 , pp. 691-702
    • Goffeau, A.1    Slonimski, P.2    Nakai, K.3    Risler, J.L.4
  • 48
    • 0028902788 scopus 로고
    • Prediction of helical transmembrane segments at 95% accuracy
    • Rost, B., Fariselli, P., Casadio, R., Sander, C. Prediction of helical transmembrane segments at 95% accuracy. Protein Sci. 4:521-533, 1995.
    • (1995) Protein Sci. , vol.4 , pp. 521-533
    • Rost, B.1    Fariselli, P.2    Casadio, R.3    Sander, C.4
  • 49
    • 0029889988 scopus 로고    scopus 로고
    • PHD: Predicting one-dimensional protein secondary structure by profile-based neural networks
    • Rost, B. PHD: predicting one-dimensional protein secondary structure by profile-based neural networks. Methods Enzymol. 266:525-539, 1996.
    • (1996) Methods Enzymol. , vol.266 , pp. 525-539
    • Rost, B.1
  • 50
    • 0030837927 scopus 로고    scopus 로고
    • Are there dominant membrane protein families with a given number of helices?
    • Arkin, I., Brunger, A., Engelman, D. Are there dominant membrane protein families with a given number of helices? Proteins 28:465-466, 1997.
    • (1997) Proteins , vol.28 , pp. 465-466
    • Arkin, I.1    Brunger, A.2    Engelman, D.3
  • 51
    • 0031892162 scopus 로고    scopus 로고
    • How many membrane proteins are there?
    • Boyd, D., Schierle, C., Beckwith, J. How many membrane proteins are there? Protein Sci. 7:201-205, 1998.
    • (1998) Protein Sci. , vol.7 , pp. 201-205
    • Boyd, D.1    Schierle, C.2    Beckwith, J.3
  • 52
    • 0032570779 scopus 로고    scopus 로고
    • Do transmembrane protein superfolds exist?
    • Jones, D.T. Do transmembrane protein superfolds exist? FEBS Lett. 423:281-285, 1998.
    • (1998) FEBS Lett. , vol.423 , pp. 281-285
    • Jones, D.T.1
  • 53
    • 0030835739 scopus 로고    scopus 로고
    • The complete genome sequence of the gastric pathogen Helicobacter pylori
    • Tomb, J.-F., White, O., Kerlavage, A.R., et al. The complete genome sequence of the gastric pathogen Helicobacter pylori. Nature 388:539-547, 1997.
    • (1997) Nature , vol.388 , pp. 539-547
    • Tomb, J.-F.1    White, O.2    Kerlavage, A.R.3
  • 54
    • 0031470826 scopus 로고    scopus 로고
    • Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi
    • Fraser, C.M., Casjens, S., Huang, W.M., et al. Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi [see comments]. Nature 390:580-586, 1997.
    • (1997) Nature , vol.390 , pp. 580-586
    • Fraser, C.M.1    Casjens, S.2    Huang, W.M.3
  • 55
    • 0031954925 scopus 로고    scopus 로고
    • Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms
    • Wallin, E., von Heijne, G. Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms [In Process Citation]. Protein Sci 7:1029-1038, 1998.
    • (1998) Protein Sci , vol.7 , pp. 1029-1038
    • Wallin, E.1    Von Heijne, G.2
  • 57
    • 0029785147 scopus 로고    scopus 로고
    • Mapping the protein universe
    • Holm, L., Sander, C. Mapping the protein universe. Science 273:595-602, 1996.
    • (1996) Science , vol.273 , pp. 595-602
    • Holm, L.1    Sander, C.2
  • 58
    • 0028961335 scopus 로고
    • SCOP: A structural classification of proteins for the investigation of sequences and structures
    • Murzin, A., Brenner, S.E., Hubbard, T., Chothia, C. SCOP: a structural classification of proteins for the investigation of sequences and structures. J. Mol. Biol. 247:536-540, 1995.
    • (1995) J. Mol. Biol. , vol.247 , pp. 536-540
    • Murzin, A.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4
  • 59
    • 0028593509 scopus 로고
    • Protein super-families and domain superfolds
    • Orengo, C.A., Jones, D.T., Thornton, J.M. Protein super-families and domain superfolds. Nature 372:631-634, 1994.
    • (1994) Nature , vol.372 , pp. 631-634
    • Orengo, C.A.1    Jones, D.T.2    Thornton, J.M.3
  • 60
    • 0031022601 scopus 로고    scopus 로고
    • LPFC: An Internet library of protein family core structures
    • Schmidt, R. Gerstein, M., Altman, R. LPFC: an Internet library of protein family core structures. Protein Sci. 6:246-248, 1997.
    • (1997) Protein Sci. , vol.6 , pp. 246-248
    • Schmidt, R.1    Gerstein, M.2    Altman, R.3
  • 61
    • 0026511848 scopus 로고
    • A databank merging related protein structures and sequences
    • Pascarella, S., Argos, P. A databank merging related protein structures and sequences. Protein Eng. 5:121-137, 1992.
    • (1992) Protein Eng. , vol.5 , pp. 121-137
    • Pascarella, S.1    Argos, P.2
  • 62
    • 0026030641 scopus 로고
    • Database of homology-derived protein structures and the structural meaning of sequence alignment
    • Sander, C., Schneider, R. Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins 9:56-68, 1991.
    • (1991) Proteins , vol.9 , pp. 56-68
    • Sander, C.1    Schneider, R.2
  • 64
    • 0026331041 scopus 로고
    • Molecular architecture and electrostatic properties of a bacterial porin
    • Weiss, M.S., Abele, U., Weckesser, J., Welte, W., Schiltz, E., Schulz, G.E. Molecular architecture and electrostatic properties of a bacterial porin. Science 254:1627-1630, 1991.
    • (1991) Science , vol.254 , pp. 1627-1630
    • Weiss, M.S.1    Abele, U.2    Weckesser, J.3    Welte, W.4    Schiltz, E.5    Schulz, G.E.6
  • 65
    • 0029901640 scopus 로고    scopus 로고
    • Analysis of compositionally biased regions in sequence databases
    • Wootton, J.C., Federhen, S. Analysis of compositionally biased regions in sequence databases. Methods Enzymol. 266:554-571, 1996.
    • (1996) Methods Enzymol. , vol.266 , pp. 554-571
    • Wootton, J.C.1    Federhen, S.2
  • 66
    • 0031039160 scopus 로고    scopus 로고
    • Sequence analysis and recombinant expression of a 28-kilodalton Treponema pallidum subsp. pallidum rare outer membrane protein (Tromp2)
    • Champion, C.I., Blanco, D.R., Exner, M.M., et al. Sequence analysis and recombinant expression of a 28-kilodalton Treponema pallidum subsp. pallidum rare outer membrane protein (Tromp2). J. Bacteriol. 179:1230-1238, 1997.
    • (1997) J. Bacteriol. , vol.179 , pp. 1230-1238
    • Champion, C.I.1    Blanco, D.R.2    Exner, M.M.3
  • 67
    • 0030847766 scopus 로고    scopus 로고
    • Protein Data Bank archives of three-dimensional macromolecular structures
    • Abola, E., Sussman, J., Prilusky, J., Manning, N. Protein Data Bank archives of three-dimensional macromolecular structures. Methods Enzymol. 277:556-571, 1997.
    • (1997) Methods Enzymol. , vol.277 , pp. 556-571
    • Abola, E.1    Sussman, J.2    Prilusky, J.3    Manning, N.4
  • 68
    • 0030983386 scopus 로고    scopus 로고
    • Population statistics of protein structures: Lessons from structural classifications
    • Brenner, S.E., Chothia, C., Hubbard, T.J. Population statistics of protein structures: lessons from structural classifications [In Process Citation]. Curr. Opin. Struct. Biol. 7:369-376, 1997.
    • (1997) Curr. Opin. Struct. Biol. , vol.7 , pp. 369-376
    • Brenner, S.E.1    Chothia, C.2    Hubbard, T.J.3
  • 69
    • 0029006062 scopus 로고
    • The multiplicity of domains in proteins
    • Doolittle, R.F. The multiplicity of domains in proteins. [Review]. Annu. Rev. Biochem. 64:287-314, 1995.
    • (1995) Annu. Rev. Biochem. , vol.64 , pp. 287-314
    • Doolittle, R.F.1
  • 71
    • 0029772552 scopus 로고    scopus 로고
    • Emergence of preferred structures in a simple model of protein folding
    • Li, H., Helling, R., Tang, C., Wingreen, N. Emergence of preferred structures in a simple model of protein folding [see comments]. Science 273:666-669, 1996.
    • (1996) Science , vol.273 , pp. 666-669
    • Li, H.1    Helling, R.2    Tang, C.3    Wingreen, N.4
  • 72
    • 0031468610 scopus 로고    scopus 로고
    • Analysis of protein domain families in Caenorhabditis elegans
    • Sonnhammer, E.L., Durbin, R. Analysis of protein domain families in Caenorhabditis elegans. Genomics 46:200-216, 1997.
    • (1997) Genomics , vol.46 , pp. 200-216
    • Sonnhammer, E.L.1    Durbin, R.2
  • 73
    • 0030597980 scopus 로고    scopus 로고
    • The emergence of major cellular processes in evolution
    • Ouzounis, C., Kyrpides, N. The emergence of major cellular processes in evolution. FEBS Lett. 390:119-123, 1996.
    • (1996) FEBS Lett. , vol.390 , pp. 119-123
    • Ouzounis, C.1    Kyrpides, N.2
  • 75
    • 0028055018 scopus 로고
    • The winds of (evolutionary) change: Breathing new life into microbiology
    • Olsen, G.J., Woese, C.R., Overbeek, R. The winds of (evolutionary) change: breathing new life into microbiology. J. Bacteriol. 176:1-6, 1994.
    • (1994) J. Bacteriol. , vol.176 , pp. 1-6
    • Olsen, G.J.1    Woese, C.R.2    Overbeek, R.3
  • 76
    • 0030838058 scopus 로고    scopus 로고
    • A bug with excess gastric avidity
    • Doolittle, R.F. A bug with excess gastric avidity [news; comment]. Nature 388:515-516, 1997.
    • (1997) Nature , vol.388 , pp. 515-516
    • Doolittle, R.F.1
  • 77
    • 0017309766 scopus 로고
    • Structural patterns in globular proteins
    • Levitt, M., Chothia, C. Structural patterns in globular proteins. Nature 261:552-558, 1976.
    • (1976) Nature , vol.261 , pp. 552-558
    • Levitt, M.1    Chothia, C.2
  • 78
    • 0031442518 scopus 로고    scopus 로고
    • Characterization of the yeast transcriptome
    • Velculescu, V.E., Zhang, L., Zhou, W., et al. Characterization of the yeast transcriptome. Cell 88:243-251, 1997.
    • (1997) Cell , vol.88 , pp. 243-251
    • Velculescu, V.E.1    Zhang, L.2    Zhou, W.3
  • 79
    • 0030699475 scopus 로고    scopus 로고
    • Yeast microarrays for genome wide parallel genetic and gene expression analysis
    • Lashkari, D.A., DeRisi, J.L., McCusker, J.H., et al. Yeast microarrays for genome wide parallel genetic and gene expression analysis. Proc. Natl. Acad. Sci. USA 94:13057-13062, 1997.
    • (1997) Proc. Natl. Acad. Sci. USA , vol.94 , pp. 13057-13062
    • Lashkari, D.A.1    DeRisi, J.L.2    McCusker, J.H.3
  • 80
    • 0030669030 scopus 로고    scopus 로고
    • Exploring the metabolic and genetic control of gene expression on a genomic scale
    • DeRisi, J.L., Iyer, V.R., Brown, P.O. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278:680-686, 1997.
    • (1997) Science , vol.278 , pp. 680-686
    • DeRisi, J.L.1    Iyer, V.R.2    Brown, P.O.3
  • 82
    • 0029070982 scopus 로고
    • Noncoding DNA, Zipf's law, and language
    • Konopka, A.K., Martindale, C. Noncoding DNA, Zipf's law, and language [letter]. Science 268:789, 1995.
    • (1995) Science , vol.268 , pp. 789
    • Konopka, A.K.1    Martindale, C.2
  • 83
    • 0028569766 scopus 로고
    • Hints of a language in junk DNA
    • Flam, F. Hints of a language in junk DNA [news] [see comments]. Science 266:1320, 1994.
    • (1994) Science , vol.266 , pp. 1320
    • Flam, F.1
  • 84
    • 0030782481 scopus 로고    scopus 로고
    • How are model protein structures distributed in sequence space?
    • Bornberg-Bauer, E. How are model protein structures distributed in sequence space? [In Process Citation]. Biophys. J. 73:2393-2403, 1997.
    • (1997) Biophys. J. , vol.73 , pp. 2393-2403
    • Bornberg-Bauer, E.1
  • 85
  • 87
    • 15444350252 scopus 로고    scopus 로고
    • The complete genome sequence of Escherichia coli K-12
    • Blattner, F.R., Plunkett, G.P., III, Bloch, C.A., et al. The complete genome sequence of Escherichia coli K-12. Science 277:1453-1462, 1997.
    • (1997) Science , vol.277 , pp. 1453-1462
    • Blattner, F.R.1    Plunkett III, G.P.2    Bloch, C.A.3
  • 89
    • 0031832807 scopus 로고    scopus 로고
    • Transposable elements and genome organization: A comprehensive survey of retrotransposons revealed by the complete Saccharomyces cereuisiae genome sequence
    • Kim, J.M., Vanguri, S., Boeke, J.D., Gabriel, A., Voytas., D.F. Transposable elements and genome organization: a comprehensive survey of retrotransposons revealed by the complete Saccharomyces cereuisiae genome sequence. Genome Res. 8:464-478, 1998.
    • (1998) Genome Res. , vol.8 , pp. 464-478
    • Kim, J.M.1    Vanguri, S.2    Boeke, J.D.3    Gabriel, A.4    Voytas, D.F.5
  • 90
    • 0029637588 scopus 로고
    • PDBbrowse - A graphics interface to the Brookhaven Protein Data Bank
    • Stampf, D.R., Felder, C.E., Sussman, J.L. PDBbrowse - a graphics interface to the Brookhaven Protein Data Bank. Nature 374:572-574, 1995.
    • (1995) Nature , vol.374 , pp. 572-574
    • Stampf, D.R.1    Felder, C.E.2    Sussman, J.L.3
  • 95
    • 0345130783 scopus 로고
    • Analysis of a Bacillus subtilis genome fragment using a co-operative computer system prototype
    • Medigue., C., Moszer, I., Viari, A., Danchin, A. Analysis of a Bacillus subtilis genome fragment using a co-operative computer system prototype. Gene 165:GC37-51, 1995.
    • (1995) Gene , vol.165
    • Medigue, C.1    Moszer, I.2    Viari, A.3    Danchin, A.4
  • 96
    • 0021919480 scopus 로고
    • Rapid and sensitive protein similarity searches
    • Lipman, D.J., Pearson, W.R. Rapid and sensitive protein similarity searches. Science 227:1435-1441, 1985.
    • (1985) Science , vol.227 , pp. 1435-1441
    • Lipman, D.J.1    Pearson, W.R.2
  • 97
    • 0023989064 scopus 로고
    • Improved tools for biological sequence analysis
    • Pearson, W.R., Lipman, D.J. Improved tools for biological sequence analysis. Proc. Natl. Acad. Sci. USA 85:2444-2448, 1988.
    • (1988) Proc. Natl. Acad. Sci. USA , vol.85 , pp. 2444-2448
    • Pearson, W.R.1    Lipman, D.J.2
  • 98
    • 0032568596 scopus 로고    scopus 로고
    • Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships
    • Brenner, S., Chothia, C., Hubbard, T. Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships. Proc. Natl. Acad. Sci. USA 95:6073-6078, 1998.
    • (1998) Proc. Natl. Acad. Sci. USA , vol.95 , pp. 6073-6078
    • Brenner, S.1    Chothia, C.2    Hubbard, T.3
  • 99
    • 0032512799 scopus 로고    scopus 로고
    • Empirical statistical estimates for sequence similarity searches
    • Pearson, W.R. Empirical statistical estimates for sequence similarity searches. J. Mol. Biol. 276:71-84, 1998.
    • (1998) J. Mol. Biol. , vol.276 , pp. 71-84
    • Pearson, W.R.1
  • 100
    • 0029933671 scopus 로고    scopus 로고
    • Effective protein sequence comparison
    • Pearson, W.R. Effective protein sequence comparison. Methods Enzymol. 266:227-259, 1996.
    • (1996) Methods Enzymol. , vol.266 , pp. 227-259
    • Pearson, W.R.1
  • 101
    • 0030776390 scopus 로고    scopus 로고
    • Identifying distantly related protein sequences
    • Pearson, W.R. Identifying distantly related protein sequences. Comput. Appl. Biosci. 13:325-332, 1997.
    • (1997) Comput. Appl. Biosci. , vol.13 , pp. 325-332
    • Pearson, W.R.1
  • 102
    • 0032568649 scopus 로고    scopus 로고
    • A unified statistical framework for sequence comparison and structure comparison
    • Levitt, M., Gerstein, M. A unified statistical framework for sequence comparison and structure comparison. Proc. Natl. Acad. Sci. USA 95:5913-5920, 1998.
    • (1998) Proc. Natl. Acad. Sci. USA , vol.95 , pp. 5913-5920
    • Levitt, M.1    Gerstein, M.2
  • 104
    • 0027175241 scopus 로고
    • Applications and statistics for multiple high-scoring segments in molecular sequences
    • Karlin, S., Altschul, S.F. Applications and statistics for multiple high-scoring segments in molecular sequences. Proc. Natl. Aad. Sci. USA 90:5873-5877, 1993.
    • (1993) Proc. Natl. Aad. Sci. USA , vol.90 , pp. 5873-5877
    • Karlin, S.1    Altschul, S.F.2
  • 106
    • 0030028728 scopus 로고    scopus 로고
    • Principles of protein-protein interactions
    • Jones, S., Thornton, J. Principles of protein-protein interactions. Proc. Natl. Acad. Sci. USA 93:13-20, 1996.
    • (1996) Proc. Natl. Acad. Sci. USA , vol.93 , pp. 13-20
    • Jones, S.1    Thornton, J.2
  • 108
    • 0028091659 scopus 로고
    • Detection of conserved segments in proteins: Iterative scanning of sequence databases with alignment blocks
    • Tatusov, R.L., Altschul, S.F., Koonin, E.V. Detection of conserved segments in proteins: iterative scanning of sequence databases with alignment blocks. Proc. Natl. Acad. Sci. USA 91:12091-12095, 1994.
    • (1994) Proc. Natl. Acad. Sci. USA , vol.91 , pp. 12091-12095
    • Tatusov, R.L.1    Altschul, S.F.2    Koonin, E.V.3
  • 109
    • 0029047319 scopus 로고
    • Prediction of protein folding class using global description of amino acid sequence
    • Dubchak, I., Muchnik, I., Holbrook, S.R., Kim, S.H. Prediction of protein folding class using global description of amino acid sequence. Proc. Natl. Acad. Sci. USA 92:8700-8704, 1995.
    • (1995) Proc. Natl. Acad. Sci. USA , vol.92 , pp. 8700-8704
    • Dubchak, I.1    Muchnik, I.2    Holbrook, S.R.3    Kim, S.H.4
  • 110
    • 0032539805 scopus 로고    scopus 로고
    • Seeking an ancient enzyme in Methanococcus jannaschii using ORF, a program based on predicted secondary structure comparisons
    • Aurora, R., Rose, G.D. Seeking an ancient enzyme in Methanococcus jannaschii using ORF, a program based on predicted secondary structure comparisons. Proc. Natl. Acad. Sci. USA 95:2818-2823, 1998.
    • (1998) Proc. Natl. Acad. Sci. USA , vol.95 , pp. 2818-2823
    • Aurora, R.1    Rose, G.D.2
  • 111
    • 0027092678 scopus 로고
    • Selection of a representative set of structures from the Brookhaven Protein Data Bank
    • Hobohm, U., Scharf, M., Schneider, R., Sander, C. Selection of a representative set of structures from the Brookhaven Protein Data Bank. Protein Sci. 1:409-417, 1992.
    • (1992) Protein Sci. , vol.1 , pp. 409-417
    • Hobohm, U.1    Scharf, M.2    Schneider, R.3    Sander, C.4
  • 112
    • 0028205447 scopus 로고
    • Enlarged representative set of protein structures
    • Hobohm, U., Sander, C. Enlarged representative set of protein structures. Protein Sci. 3:522, 1994.
    • (1994) Protein Sci. , vol.3 , pp. 522
    • Hobohm, U.1    Sander, C.2
  • 113
    • 0026661145 scopus 로고
    • Selection of a representative set of structures from Brookhaven Protein Data Bank
    • Boberg, J., Salakoski, T., Vihinen, M. Selection of a representative set of structures from Brookhaven Protein Data Bank. Proteins 14:265-276, 1992.
    • (1992) Proteins , vol.14 , pp. 265-276
    • Boberg, J.1    Salakoski, T.2    Vihinen, M.3
  • 115
    • 0000122573 scopus 로고
    • PHYLIP-Phylogeny Inference Package (Version 3.2)
    • Felsenstein, J. PHYLIP-Phylogeny Inference Package (Version 3.2). Cladistics 5:164-166, 1989.
    • (1989) Cladistics , vol.5 , pp. 164-166
    • Felsenstein, J.1
  • 117
    • 0022510143 scopus 로고
    • Identifying nonpolar transbilayer helices in amino acid sequences of membrane proteins
    • Engelman, D.M., Steitz, T.A., Goldman, A. Identifying nonpolar transbilayer helices in amino acid sequences of membrane proteins. [Review]. Annu. Rev. Biophys. Biophys. Chem, 15:321-353, 1986.
    • (1986) Annu. Rev. Biophys. Biophys. Chem , vol.15 , pp. 321-353
    • Engelman, D.M.1    Steitz, T.A.2    Goldman, A.3
  • 118
    • 0001514262 scopus 로고
    • Statistics of local complexity in amino acid sequences and sequence databases
    • Wootton, J.C., Federhen, S. Statistics of local complexity in amino acid sequences and sequence databases. Comput. Chem. 17:149-163, 1993.
    • (1993) Comput. Chem. , vol.17 , pp. 149-163
    • Wootton, J.C.1    Federhen, S.2
  • 119
    • 0028501914 scopus 로고
    • Non-globular domains in protein sequences: Automated segmentation using complexity measures
    • Wootton, J.C. Non-globular domains in protein sequences: automated segmentation using complexity measures. Comput. Chem. 18:269-285, 1994.
    • (1994) Comput. Chem. , vol.18 , pp. 269-285
    • Wootton, J.C.1
  • 120
    • 0028829125 scopus 로고
    • The minimal gene complement of Mycoplasma genitalium
    • Fraser, C.M., Gocayne, J.D., White, O., et al. The minimal gene complement of Mycoplasma genitalium [see comments]. Science 270:397-403, 1995.
    • (1995) Science , vol.270 , pp. 397-403
    • Fraser, C.M.1    Gocayne, J.D.2    White, O.3
  • 121
    • 16044367245 scopus 로고    scopus 로고
    • Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii
    • Bult, C.J., White, O., Olsen, G.J., et al. Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science 273:1058-1073, 1996.
    • (1996) Science , vol.273 , pp. 1058-1073
    • Bult, C.J.1    White, O.2    Olsen, G.J.3
  • 123
    • 0031589946 scopus 로고    scopus 로고
    • The Yeast Genome Directory
    • Goffeau, A., Aert, R., Agostini-Carbone, M.L., et al. The Yeast Genome Directory. Nature 387(Suppl.):5-105, 1997.
    • (1997) Nature , vol.387 , Issue.SUPPL. , pp. 5-105
    • Goffeau, A.1    Aert, R.2    Agostini-Carbone, M.L.3
  • 124
    • 0030606607 scopus 로고    scopus 로고
    • Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions
    • Kaneko, T., Sato, S., Kotani, H., et al. Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions. DNA Res. 3:109-136, 1996.
    • (1996) DNA Res. , vol.3 , pp. 109-136
    • Kaneko, T.1    Sato, S.2    Kotani, H.3
  • 125
  • 126
    • 0026244229 scopus 로고
    • MOLSCRIPT - A program to produce both detailed and schematic plots of protein structures
    • Kraulis, P.J. MOLSCRIPT - a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24:946-950, 1991.
    • (1991) J. Appl. Crystallogr. , vol.24 , pp. 946-950
    • Kraulis, P.J.1
  • 127
    • 0031734751 scopus 로고    scopus 로고
    • Comparing microbial genomes in terms of protein structure: Surveys of a finite parts list
    • in press
    • Gerstein, M., Hegyi, H. Comparing microbial genomes in terms of protein structure: Surveys of a finite parts list. FEMS Microbiol. Rev. 1998, in press.
    • (1998) FEMS Microbiol. Rev.
    • Gerstein, M.1    Hegyi, H.2
  • 128
    • 0032411225 scopus 로고    scopus 로고
    • How representative are the known structures of the proteins in a complete genome? A comprehensive structural census
    • in press
    • Gerstein, M. How representative are the known structures of the proteins in a complete genome? A comprehensive structural census. Folding & Design 1998, in press.
    • (1998) Folding & Design
    • Gerstein, M.1


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