Comparing genomes in terms of protein structure: Surveys of a finite parts list

FEMS Microbiology Reviews

Volumn 22, Issue 4, 1998, Pages 277-304

  Gerstein, Mark ^a   Hegyi, Hedi ^a  

^a YALE UNIVERSITY   (United States)

Author keywords

Bioinformatics; Databank census; Protein fold

Indexed keywords

CLASSIFICATION; DATA BASE; GENETIC PROCEDURES; GENOME; INFORMATION; MICROBIAL GENETICS; NONHUMAN; PROTEIN FOLDING; PROTEIN STRUCTURE; REVIEW;

EID: 0031734751     PISSN: 01686445     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0168-6445(98)00019-9     Document Type: Article

References (208)

1. Nowak, R. (1995) Bacterial genome sequence bagged. Science 269, 468-470.
2. Langreth, R. (1997) Scientists unlock sequence of ulcer bacterium's genes. Wall Street Journal B1.
3. Wade, N. (1997) Thinking small paying off big in gene quest. New York Times, 3 February 1997, A1 (front page).
4. Fleischmann, R.D. et al. (1995) Whole-genome random sequencing and assembly of haemophilus influenzae rd. Science 269, 496-512.
5. Goffeau, A. et al. (1997) The yeast genome directory. Nature 387 (Suppl.), 5-105.
6. Brenner, S.E., Chothia, C. and Hubbard, T.J. (1997) Population statistics of protein structures: lessons from structural classifications. Curr. Opin. Struct. Biol. 7, 369-376.
7. Murzin, A., Brenner, S.E., Hubbard, T. and Chothia, C. (1995) SCOP: a structural classification of proteins for the investigation of sequences and structures. J. Mol. Biol. 247, 536-540.
8. Holm, L. and Sander, C. (1996) Mapping the protein universe. Science 273, 595-602.
9. Holm, L. and Sander, C. (1997) New structure - novel fold? Structure 5, 165-171.
10. Orengo, C.A., Michie, A.D., Jones, S., Jones, D.T., Swindells, M.B. and Thornton, J.M. (1997) CATH - a hierarchic classification of protein domain structures. Structure 5, 1093-1108.
11. Chothia, C. (1992) Proteins - 1000 families for the molecular biologist. Nature 357, 543-544.
12. Shapiro, L. and Lima, C.D. (1998) The Argonne Structural Genomics Workshop: Lamaze class for the birth of a new science. Structure 6, 265-267.
13. Pennisi, E. (1998) Taking a structured approach to understanding proteins [news]. Science 279, 978-979.
14. Holmgren, A. and Branden, C.I. (1989) Crystal structure of chaperone protein PapD reveals an immunoglobulin fold. Nature 342, 248-251.
15. Berg, J.M. and Shi, Y. (1996) The galvanization of biology: a growing appreciation for the roles of zinc. Science 217, 1081-1085.
16. Blaisdell, B.E., Campbell, A.M. and Karlin, S. (1996) Similarities and dissimilarities of phage genomes. Proc. Natl. Acad. Sci. USA 93, 5854-5859.
17. Karlin, S. and Burge, C. (1995) Dinucleotide relative abundance extremes: a genomic signature [Review]. Trends Genet. 11, 283-290.
18. Karlin, S., Burge, C. and Campbell, A.M. (1992) Statistical analyses of counts and distributions of restriction sites in DNA sequences. Nucleic Acids Res. 20, 1363-1370.
19. Karlin, S., Mrazek, J. and Campbell, A.M. (1996) Frequent oligonucleotides and peptides of the haemophilus influenzae genome. Nucleic Acids Res. 24, 4263-4272.
20. Koonin, E.V., Mushegian, A.R. and Rudd, K.E. (1996) Sequencing and analysis of bacterial genomes. Curr. Biol. 6, 404-416.
21. Brenner, S., Hubbard, T., Murzin, A. and Chothia, C. (1995) Gene duplication in H. Influenzae. Nature 378, 140.
22. Riley, M. (1997) Genes and proteins of Escherichia coli K-12 (GenProtEC). Nucleic Acids Res. 25, 51-52.
23. Wolfe, K.H. and Shields, D.C. (1997) Molecular evidence for an ancient duplication of the entire yeast genome. Nature 387, 708-713.
24. Gerstein (1997) A structural census of genomes: comparing eukaryotic, bacterial and archaeal genomes in terms of protein structure. J. Mol. Biol. 274, 562-576.
25. Tamames, J., Casari, G., Ouzounis, C. and Valencia, A. (1997) Conserved clusters of functionally related genes in two bacterial genomes. J. Mol. Evol. 44, 66-73.
26. Green, P., Lipman, D., Hillier, L., Waterston, R., States, D. and Claverie, J.M. (1993) Ancient conserved regions in new gene sequences and the protein databases. Science 259, 1711-1716.
27. Koonin, E.V., Tatusov, R.L. and Rudd, K.E. (1995) Sequence similarity analysis of Escherichia coli proteins: functional and evolutionary implications. Proc. Natl. Acad. Sci. USA 92, 11921-11925.
28. Tatusov, R.L., Koonin, E.V. and Lipman, D.J. (1997) A genomic perspective on protein families. Science 278, 631-637.
29. Ouzounis, C., Kyrpides, N. and Sander, C. (1995) Novel protein families in Archaean genomes. Nucleic Acids Res. 23, 565-570.
30. Clayton, R.A., White, O., Ketchum, K.A. and Venter, J.C. (1997) The first genome from the third domain of life [news]. Nature 387, 459-462.
31. Bork, P., Ouzounis, C., Sander, C., Scharf, M., Schneider, R. and Sonnhammer, E. (1992) What's in a genome? Nature 358, 287.
32. Bork, P., Ouzounis, C., Sander, C., Scharf, M., Schneider, R. and Sonnhammer, E. (1992) Comprehensive sequence analysis of the 182 predicted open reading frames of yeast chromosome iii. Protein Sci. 1, 1677-1690.
33. Scharf, M., Schneider, R., Casari, G., Bork, P., Valencia, A., Ouzounis, C. and Sander, C. (1994) GeneQuiz: a workbench for sequence analysis. In : Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 348-353. AAAI Press, Menlo Park, CA.
34. Casari, G. et al. (1995) Challenging times for bioinformatics. Nature 376, 647-648.
35. Ouzounis, C., Bork, P., Casari, G. and Sander, C. (1995) New protein functions in yeast chromosome VIII. Protein Sci. 4, 2424-2428.
36. Gaasterland, T. and Sensen, C.W. (1996) Fully automated genome analysis that reflects user needs and preferences. A detailed introduction to the MAGPIE system architecture. Biochimie 78, 302-310.
37. Huynen, M.A., Diaz-Lazcoz, Y. and Bork, P. (1997) Differential genome display [letter]. Trends Genet. 13, 389-390.
38. Tomb, J.-F. et al. (1997) The complete genome sequence of the gastric pathogen Helicobacter pylori. Nature 388, 539-547.
39. Fraser, C.M. et al. (1997) Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi. Nature 390, 580-586.
40. Karp, P., Riley, M., Paley, S. and Pellegrini-Toole, A. (1996) EcoCyc: electronic encyclopedia of E. coli genes and metabolism. Nucleic Acids Res. 24, 32-40.
41. Mushegian, A.R. and Koonin, E.V. (1996) A minimal gene set for cellular life derived by comparison of complete bacterial genomes. Proc. Natl. Acad. Sci. USA 93, 10268-10273.
42. Koonin, E.V., Tatusov, R.L. and Rudd, K.E. (1996) Protein sequence comparison at a genome scale. Methods Enzymol. 266, 295-322.
43. Tang, C.M., Hood, D.W. and Moxon, E.R. (1997) Haemophilus influence : the impact of whole genome sequencing on microbiology. Trends Genet. 13, 399-404.
44. Tatusov, R.L. et al. (1996) Metabolism and evolution of Haemophilus influenzae deduced from a whole-genome comparison with Escherichia coli. Curr. Biol. 6, 279-291.
45. Henikoff, S. and Henikoff, J.G. (1993) Automated assembly of protein blocks for database searching. Proc. Natl. Acad. Sci. USA 19, 6565-6572.
46. Henikoff, S. and Henikoff, J.G. (1994) Protein family classification based on searching a database of blocks. Genomics 19, 97-107.
47. Henikoff, S., Greene, E.A., Pietrokovski, S., Bork, P., Attwood, T.K. and Hood, L. (1997) Gene families: the taxonomy of protein paralogs and chimeras. Science 278, 609-614.
48. Henikoff, S., Pietrokovski, S. and Henikoff, J.G. (1998) Superior performance in protein homology detection with the Blocks Database servers. Nucleic Acids Res. 26, 309-312.
49. Sonnhammer, E.L.L. and Kahn, D. (1994) Modular arrangement of proteins as inferred from analysis of homology. Protein Sci. 3, 482-492.
50. Riley, M. and Labedan, B. (1997) 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.
51. Fabian, P., Murvai, J., Hatsagi, Z., Vlahovicek, K., Hegyi, H. and Pongor, S. (1997) The SBASE protein domain library, release 5.0: a collection of annotated protein sequence segments. Nucleic Acids Res. 25, 240-243.
52. Corpet, F., Gouzy, J. and Kahn, D. (1998) The ProDom database of protein domain families. Nucleic Acids Res. 26, 323-326.
53. Sonnhammer, E.L., Eddy, S.R., Birney, E., Bateman, A. and Durbin, R. (1998) Pfam: multiple sequence alignments and HMM-profiles of protein domains. Nucleic Acids Res. 26, 320-322.
54. Sonnhammer, E.L., Eddy, S.R. and Durbin, R. (1997) Pfam: a comprehensive database of protein domain families based on seed alignments. Proteins 28, 405-420.
55. Tatusov, R.L., Altschul, S.F. and Koonin, E.V. (1994) Detection of conserved segments in proteins : iterative scanning of sequence databases with alignment blocks. Proc. Natl. Acad. Sci. USA 91, 12091-12095.
56. Bairoch, A., Bucher, P. and Hofmann, K. (1997) The PROSITE database, its status in 1997. Nucleic Acids Res. 25, 217-221.
57. Attwood, T.K., Beck, M.E., Flower, D.R., Scordis, P. and Selley, J.N. (1998) The PRINTS protein fingerprint database in its fifth year. Nucleic Acids Res. 26, 304-308.
58. Neuwald, A.F., Liu, J.S. and Lawrence, C.E. (1995) Gibbs motif sampling: detection of bacterial outer membrane protein repeats. Protein Sci. 4, 1618-1632.
59. Onuchic, J.N., Luthey-Schulten, Z. and Wolynes, P.G. (1997) Theory of protein folding: the energy landscape perspective. Annu. Rev. Phys. Chem. 48, 545-600.
60. Panchenko, A.R., Luthey-Schulten, Z., Cole, R. and Wolynes, P.G. (1997) The foldon universe: a survey of structural similarity and self-recognition of independently folding units. J. Mol. Biol. 272, 95-105.
61. Panchenko, A.R., Luthey-Schulten, Z. and Wolynes, P.G. (1996) Foldons, protein structural modules, and exons. Proc. Natl. Acad. Sci. USA 93, 2008-2013.
62. Gerstein, M. and Altman, R. (1995) Average core structures and variability measures for protein families: application to the immunoglobulins. J. Mol. Biol. 251, 161-175.
63. Gerstein, M. and Altman, R. (1995) A structurally invariant core for the globins. CABIOS 11, 633-644.
64. Chothia, C. and Lesk, A.M. (1986) The relation between the divergence of sequence and structure in proteins. EMBO J. 5, 823-826.
65. Chothia, C. and Gerstein, M. (1997) Protein evolution. How far can sequences diverge? Nature 385, 579-581.
66. Lesk, A.M., Levitt, M. and Chothia, C. (1986) Alignment of amino acid sequences of distantly related proteins using variable gap penalties. Protein Eng. 1, 77-78.
67. Brenner, S., Chothia, C. and Hubbard, T. (1998) Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships. Proc. Natl. Acad. Sci. USA 95, 6073-6078.
68. Dalal, S., Balasubramanian, S. and Regan, L. (1997) Protein alchemy: changing beta-sheet into alpha-helix. Nat. Struct. Biol. 4, 548-552.
69. Bork, P., Ouzounis, C. and Sander, C. (1994) From Genome Sequences to Protein Function. Curr. Opin. Struct. Biol. 4, 393-403.
70. Tomarev, S.I., Zinovieva, R.D. and Piatigorsky, J. (1992) Characterization of squid crystallin genes. Comparison with mammalian glutathione S-transferase genes. J. Biol. Chem. 267, 8604-8612.
71. Wilks, H.M. et al. (1988) A specific, highly active malate dehydrogenase by redesign of a lactate dehydrogenase framework. Science 242, 1541-1544.
72. Messerschmidt, A. and Wever, R. (1996) X-ray structure of a vanadium-containing enzyme: chloroperoxidase from the fungus Curvularia inaequalis. Proc. Natl. Acad. Sci. USA 93, 392-396.
73. Simons, B.H., Barnett, P., Vollenbroek, E.G., Dekker, H.L., Muijsers, A.O., Messerschmidt, A. and Wever, R. (1995) Primary structure and characterization of the vanadium chloroperoxidase from the fungus Curvularia inaequalis. Eur. J. Biochem. 229, 566-574.
74. Doolittle, R.F. (1994) Convergent evolution: the need to be explicit. Trends Biochem. Sci. 19, 15-18.
75. Lander, E.S. (1996) The genomics: global views of biology. Science 274, 536-539.
76. Remington, S.J. and Matthews, B.W. (1980) A systematic approach to the comparison of protein structures. J. Mol. Biol. 140, 77-99.
77. Satow, Y., Cohen, G.H., Padlan, E.A. and Davies, D.R. (1986) Phosphocholine binding immunoglobulin Fab McPC603. An X-ray diffraction study at 2.7 A. J. Mol. Biol. 190, 593-604.
78. Taylor, W.R., Flores, T.P. and Orengo, C.A. (1994) Multiple protein structure alignment. Protein Sci. 3, 2358-2365.
79. Artymiuk, P.J., Mitchell, E.M., Rice, D.W. and Willett, P. (1989) Searching techniques for databases of protein structures. J. Inform. Sci. 15, 287-298.
80. Sali, A. and Blundell, T. L. (1990) The definition of general topological equivalence in protein structures: a procedure involving comparison of properties and relationships through simulated annealing and dynamic programming. J. Mol. Biol. 212, 403-428.
81. Vriend, G. and Sander, C. (1991) Detection of common three-dimensional substructures in proteins. Proteins 11, 52-58.
82. Russell, R.B. and Barton, G.B. (1992) Multiple protein sequence alignment from tertiary structure comparisons. Assignment of global and residue level confidences. Proteins 14, 309-323.
83. Holm, L. and Sander, C. (1993) Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 233, 123-128.
84. Grindley, H.M., Artymiuk, P.J., Rice, D.W. and Willett, P. (1993) Identification of tertiary structure resemblance in proteins using a maximal common subgraph isomorphism algorithm. J. Mol. Biol. 229, 707-721.
85. Godzik, A. and Skolnick, J. (1994) Flexible algorithm for direct multiple alignment of protein structures and sequences. CABIOS 10, 587-596.
86. Gibrat, J.F., Madej, T. and Bryant, S.H. (1996) Surprising similarities in structure comparison. Curr. Opin. Struct. Biol. 6, 377-385.
87. Falicov, A. and Cohen, F.E. (1996) A surface of minimum area metric for the structural comparison of proteins. J. Mol. Biol. 258, 871-892.
88. Feng, Z.K. and Sippl, M.J. (1996) Optimum superimposition of protein structures: ambiguities and implications. Fold Des. 1, 123-132.
89. Cohen, G.H. (1997) ALIGN: a program to superimpose protein coordinates, accounting for insertions and deletions. J. Appl. Cryst., in press.
90. Gerstein, M. and Levitt, M. (1998) Comprehensive assessment of automatic structural alignment against a manual standard, the Scop classification of proteins. Protein Sci. 7, 445-456.
91. Doolittle, R.F. (1987) Of Urfs and Orfs. University Science Books, Mill Valley, CA.
92. Gribskov, M. and Devereux, J. (1992) Sequence Analysis Primer. Oxford University Press, New York.
93. Taylor, W.R. and Orengo, C.A. (1989) Protein structure alignment. J. Mol. Biol. 208, 1-22.
94. Levitt, M. and Gerstein, M. (1998) A unified statistical framework for sequence comparison and structure comparison. Proc. Natl. Acad. Sci. USA 95, 5913-5920.
95. Gerstein, M. and Levitt, M. (1996) Using iterative dynamic programming to obtain accurate pairwise and multiple alignments of protein structures. In : Proc. Fourth Int. Conf. on Intell. Sys. Mol. Biol. pp. 59-67. AAAI Press, Menlo Park, CA.
96. Needleman, S.B. and Wunsch, C.D. (1971) A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 48, 443-453.
97. Johnson, M.S., Sali, A. and Blundell, T.L. (1990) Phylogenetic relationships from three-dimensional protein structures. Methods Enzymol. 183, 670-691.
98. Orengo, C.A., Flores, T.P., Taylor, W.R. and Thornton, J.M. (1993) Identifying and classifying protein fold families. Protein Eng. 6, 485-500.
99. Pascarella, S. and Argos, P. (1992) A databank merging related protein structures and sequences. Protein Eng. 5, 121-137.
100. Orengo, C.A. (1994) Classification of protein folds. Curr. Opin. Struct. Biol. 4, 429-440.
101. Schmidt, R., Gerstein, M. and Altman, R. (1997) LPFC: an Internet library of protein family core structures. Protein Sci. 6, 246-248.
102. Altman, R., Hughes, C. and Gerstein, M. (1995) Methods for displaying macromolecular structural uncertainty: application to the globins. J. Mol. Graph. 13, 142-152.
103. Bryant, S.H. and Lawrence, C.E. (1993) An empirical energy function for threading protein sequence through the folding motif. Proteins Struct. Funct. Genet. 16, 92-112.
104. Hobohm, U., Scharf, M., Schneider, R. and Sander, C. (1992) Selection of a representative set of structures from the Brookhaven Protein Data Bank. Protein Sci. 1, 409-417.
105. Hobohm, U. and Sander, C. (1994) Enlarged representative set of protein structures. Protein Sci. 3, 522.
106. Boberg, J., Salakoski, T. and Vihinen, M. (1992) Selection of a representative set of structures from Brookhaven Protein Data Bank. Proteins 14, 265-276.
107. Doolittle, R.F. (1995) The multiplicity of domains in proteins [Review]. Annu. Rev. Biochem. 64, 287-314.
108. Orengo, C.A., Jones, D.T. and Thornton, J.M. (1994) Protein superfamilies and domain superfolds. Nature 372, 631-634.
109. Govindarajan, S. and Goldstein, R.A. (1996) Why are some proteins structures so common? Proc. Natl. Acad. Sci. USA 93, 3341-3345.
110. Li, H., Helling, R., Tang, C. and Wingreen, N. (1996) Emergence of preferred structures in a simple model of protein folding. Science 273, 666-669.
111. Lipman, D.J. and Pearson, W.R. (1985) Rapid and sensitive protein similarity searches. Science 227, 1435-1441.
112. Altschul, S., Gish, W., Miller, W., Myers, E.W. and Lipman, D.J. (1990) Basic local alignment search tool. J. Mol. Biol. 215, 403-410.
113. Pearson, W.R. and Lipman, D.J. (1988) Improved tools for biological sequence analysis. Proc. Natl. Acad. Sci. USA 85, 2444-2448.
114. Bairoch, A. and Apweiler, R. (1998) The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1998. Nucleic Acids Res. 26, 38-42.
115. Benson, D.A., Boguski, M., Lipman, D.J. and Ostell, J. (1996) Genbank. Nucleic Acid. Res. 24, 1-5.
116. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST : a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402.
117. Abagyan, R.A. and Batalov, S. (1997) Do aligned sequences share the same fold? J. Mol. Biol. 273, 355-368.
118. Park, J., Teichmann, S.A., Hubbard, T. and Chothia, C. (1997) Intermediate sequences increase the detection of homology between sequences. J. Mol. Biol. 273, 349-354.
119. Gerstein, M. (1998) Measurement of the gain in sensitivity in transitive sequence comparison, through an intermediate sequence. Bioinformatics, in press.
120. Krogh, A., Brown, M., Mian, I.S., Sjölander, K. and Haussler, D. (1994) Hidden Markov models in computational biology: applications to protein modelling. J. Mol. Biol. 235, 1501-1531.
121. Baldi, P., Chauvin, Y. and Hunkapiller, T. (1994) Hidden Markov models of biological primary sequence information. Proc. Natl. Acad. Sci. USA 91, 1059-1063.
122. Eddy, S.R., Mitchison, G. and Durbin, R. (1994) Maximum discrimination hidden Markov models of sequence consensus. J. Comp. Biol. 9, 9-23.
123. Taubes, G. (1996) Software matchmakers help make sense of sequences. Science 273, 588-590.
124. Bowie, J.U., Lüthy, R. and Eisenberg, D. (1991) A method to identify protein sequences that fold into a known three-dimensional structure. Science 253, 164-170.
125. Eddy, S.R. (1996) Hidden Markov models. Curr. Opin. Struct. Biol. 6, 361-365.
126. Gribskov, M., Lüthy, R. and Eisenberg, D. (1990) Profile Analysis. Methods Enzymol. 183, 146-159.
127. Smith, T.F. and Waterman, M.S. (1981) Identification of common molecular subsequences. J. Mol. Biol. 147, 195-197.
128. Blattner, F.R. et al. (1997) The complete genome sequence of Escherichia coli K-12. Science 277, 1453-1462.
129. Goffeau, A. et al. (1996) Life with 6000 genes. Science 274, 546-567.
130. Kim, J.M., Vanguri, S., Boeke, J.D., Gabriel, A. and Voytas, D.F. (1998) Transposable elements and genome organization: a comprehensive survey of retrotransposons revealed by the complete Saccharomyces cerevisiae genome sequence. Genome Res., in press.
131. Altschul, S.F. and Gish, W. (1996) Local alignment statistics. Methods Enzymol. 266, 460-480.
132. Altschul, S.F., Boguski, M.S., Gish, W. and Wootton, J.C. (1994) Issues in searching molecular sequence databases [Review]. Nat. Genet. 6, 119-129.
133. Karlin, S. and Altschul, S.F. (1993) Applications and statistics for multiple high-scoring segments in molecular sequences. Proc. Natl. Acad. Sci. USA 90, 5873-5877.
134. Karlin, S., Bucher, P., Brendel, V. and Altschul, S.F. (1991) Statistical methods and insights for protein and DNA sequences. Annu. Rev. Biophys. Biophys. Chem. 20, 175-203.
135. Karlin, S. and Altschul, S.F. (1990) Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc. Natl. Acad. Sci. USA 87, 2264-2268.
136. Pearson, W.R. (1998) Empirical statistical estimates for sequence similarity searches. J. Mol. Biol. 276, 71-84.
137. Pearson, W.R. (1996) Effective protein sequence comparison. Methods Enzymol. 266, 227-259.
138. Pearson, W.R. (1997) Identifying distantly related protein sequences. Comput. Appl. Biosci. 13, 325-332.
139. Brenner, S.E. and Hubbard, T.J.P. (1995) A specification for defining and annotating regions of macromolecular structures. In: Proc. 3rd Int. Conf. Intell. Sys. Mol. Biol. (Rawlings, C. et al., Eds.) pp. 66-71. AAAI Press, Menlo Park, CA.
140. Brenner, S., Chothia, C., Hubbard, T.J.P. and Murzin, A.G. (1996) Understanding protein structure: using Scop for fold interpretation. Methods Enzymol. 266, 635-642.
141. Frishman, D. and Mewes, H.-W. (1997) PEDANTic genome analysis. Trends Genet. 13, 415-416.
142. Bult, C.J. et al. (1996) Complete genome sequence of the methanogenic Archaeon, Methanococcus jannaschii. Science 273, 1058-1073.
143. Sonnhammer, E.L. and Durbin, R. (1997) Analysis of protein domain families in Caenorhabditis elegans. Genomics 46, 200-216.
144. Ouzounis, C. and Kyrpides, N. (1996) The emergence of major cellular processes in evolution. FEBS Lett. 390, 119-123.
145. Levitt, M. and Chothia, C. (1976) Structural patterns in globular proteins. Nature 261, 552-558.
146. Chothia, C., Hubbard, T., Brenner, S., Barns, H. and Murzin, A. (1997) Protein folds in the all-beta and all-alpha classes. Annu. Rev. Biophys. Biomol. Struct. 26, 597-627.
147. Gerstein, M. and Levitt, M. (1997) A structural census of the current population of protein sequences. Proc. Natl. Acad. Sci. USA 94, 11911-11916.
148. Rost, B. (1998) Marrying structure and genomics. Structure 6, 259-263.
149. Gerstein, M. (1998) Comparing genomes in terms of their usage of protein folds. Proteins, submitted for publication.
150. Velculescu, V.E. et al. (1997) Characterization of the yeast transcriptome. Cell 88, 243-251.
151. Lashkari, D.A. et al. (1997) Yeast microarrays for genome wide parallel genetic and gene expression analysis. Proc. Natl. Acad. Sci. USA 94, 13057-13062.
152. DeRisi, J.L., Iyer, V.R. and Brown, P.O. (1997) Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278, 680-686.
153. Bowie, J.U. and Eisenberg, D. (1993) Inverted protein structure prediction. Curr. Opin. Struct. Biol. 3, 437-444.
154. Jones, D.T. and Thornton, J.M. (1996) Potential energy functions for threading. Curr. Opin. Struct. Biol. 6, 210-216.
155. Dubchak, I., Muchnik, I., Holbrook, S.R. and Kim, S.H. (1995) Prediction of protein folding class using global description of amino acid sequence. Proc. Natl. Acad. Sci. USA 92, 8700-8704.
156. Gerstein, M., Sonnhammer, E. and Chothia, C. (1994) Volume changes on protein evolution. J. Mol. Biol. 236, 1067-1078.
157. Altschul, S.F., Carroll, R.J. and Lipman, D.J. (1989) Weights for data related by a tree. J. Mol. Biol. 207, 647-653.
158. Sander, C. and Schneider, R. (1991) Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins Struct. Funct. Genet. 9, 56-68.
159. Vingron, M. and Sibbald, P.R. (1993) Weighting in sequence space: a comparison of methods in terms of generalized sequences. Proc. Natl. Acad. Sci. USA 90, 8777-8781.
160. Miyazawa, S. and Jernigan, R.L. (1996) Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading. J. Mol. Biol. 256, 623-644.
161. Wright, T. Sampling and Census 2000: the concepts. Am. Scientist 86, 245-253.
162. Thompson, S.K. (1992) Sampling. Wiley and Sons, New York.
163. Fischer, D. and Eisenberg, D. (1997) Assigning folds to the proteins encoded by the genome of mycoplasma genitalium. Proc. Natl. Acad. Sci. USA 94, 11929-11934.
164. Rost, B. (1996) PHD: Predicting one-dimensional protein secondary structure by profile-based neural networks. Methods Enzymol. 266, 525-539.
165. Defay, T. and Cohen, F.E. (1995) Evaluation of current techniques for ab initio protein structure prediction. Proteins 23, 431-445.
166. Pedersen, J.T. and Moult, J. (1997) Ab initio protein folding simulations with genetic algorithms: simulations on the complete sequence of small proteins. Proteins Suppl. 1, 179-184.
167. Garnier, J., Gibrat, J.F. and Robson, B. (1996) GOR method for predicting protein secondary structure from amino acid sequence. Methods Enzymol. 266, 540-553.
168. Garnier, J., Osguthorpe, D. and Robson, B. (1978) Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins. J. Mol. Biol. 120, 97-120.
169. Gibrat, J., Garnier, J. and Robson, B. (1987) Further developments of protein secondary structure prediction using information theory. J. Mol. Biol. 198, 425-443.
170. Rost, B. and Sander, C. (1993) Prediction of protein secondary structure at better than 70% accuracy. J. Mol. Biol. 232, 584-599.
171. Salamov, A. and Solovyev, V. (1995) Prediction of protein secondary structure by combining nearest-neighbor algorithms and multiple sequence alignments. J. Mol. Biol. 247, 11-15.
172. King, R.D., Saqi, M., Sayle, R. and Sternberg, M.J. (1997) DSC: public domain protein secondary structure predication. Comput. Appl. Biosci. 13, 473-474.
173. Livingstone, C.D. and Barton, G.J. (1996) Identification of functional residues and secondary structure from protein multiple sequence alignment. Methods Enzymol. 266, 497-512.
174. Russell, R.B. and Barton, G.J. (1993) The limits of protein secondary structure prediction accuracy from multiple sequence alignment. J. Mol. Biol. 234, 951-957.
175. Engelman, D.M., Steitz, T.A. and Goldman, A. (1986) Identifying nonpolar transbilayer helices in amino acid sequences of membrane proteins [Review]. Annu. Rev. Biophys. Biophys. Chem. 15, 321-353.
176. Kyte, J. and Doolittle, R.F. (1982) A simple method for displaying the hydrophobic character of a protein. J. Mol. Biol. 157, 105-132.
177. Jähnig, F. (1990) Structure predictions of membrane proteins are not that bad. Trends Biochem. Sci. 15, 93-95.
178. von Heijne, G. (1994) Membrane proteins: from sequence to structure. Annu. Rev. Biophys. Biomol. Struct. 23, 167-192.
179. von Heijne, G. (1996) Principles of membrane protein assembly and structure. Prog. Biophys. Mol. Biol. 66, 113-139.
180. Persson, B. and Argos, P. (1994) Prediction of transmembrane segments in proteins utilising multiple sequence alignments. J. Mol. Biol. 237, 182-192.
181. Jones, D.T., Taylor, W.R. and Thornton, J.M. (1992) A new approach to protein fold recognition. Nature 358, 86-89.
182. Rost, B., Fariselli, P., Casadio, R. and Sander, C. (1995) Prediction of helical transmembrane segments at 95% accuracy. Protein Sci. 4, 521-533.
183. Rost, B., Fariselli, P. and Casadio, R. (1996) Topology prediction for helical transmembrane segments at 95% accuracy. Protein Sci. 7, 1704-1718.
184. Gerstein, M. (1998) Structural analysis of genomes: how representative are the known structures of the proteins in a complete genome? Folding Design, submitted for publication.
185. Frishman, D. and Mewes, H.-W. (1997) Protein structural classes in five complete genomes. Nat. Struct. Biol. 4, 626-628.
186. Goffeau, A., Slonimski, P., Nakai, K. and Risler, J.L. (1993) How many yeast genes code for membrane-spanning proteins? Yeast 9, 691-702.
187. Arkin, I., Brunger, A. and Engelman, D. (1997) Are there dominant membrane protein families with a given number of helices? Proteins 28, 465-466.
188. Boyd, D., Schierle, C. and Beckwith, J. (1998) How many membrane proteins are there? Protein Sci. 7, 201-205.
189. Jones, D.T. (1998) Do transmembrane protein superfolds exist? FEBS Lett. 423, 281-285.
190. Tomb, J.F. et al. (1997) The complete genome sequence of the gastric pathogen Helicobacter pylori [published erratum appears in Nature 1997 Sep 25; 389 (6649) 412]. Nature 388, 539-547.
191. Wallin, E. and von Heijne, G. (1998) Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms. Protein Sci. 7, 1029-1038.
192. Knuth, D. (1973) The Art of Computer Programming: Vol. 3, Sorting and Searching. Addison-Wesley, Reading, MA.
193. Konopka, A.K. and Martindale, C. (1995) Noncoding DNA, Zipf's law, and language [letter]. Science 268, 789.
194. Flam, F. (1994) Hints of a language in junk DNA [news]. Science 266, 1320.
195. Bornberg-Bauer, E. (1997) How are model protein structures distributed in sequence space? Biophys. J. 73, 2393-2403.
196. Fleischmann, R.D. et al. (1995) Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269, 496-512.
197. Fraser, C.M. et al. (1995) The minimal gene complement of Mycoplasma genitalium. Science 270, 397-403.
198. Bult, C.J. et al. (1996) Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science 273, 1058-1073.
199. Kaneko, T. et al. (1996) 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 (Suppl.), 185-209.
200. Himmelreich, R., Hubert, H., Plagens, H., Pirkl, E., Li, B.C. and Herrmann, R. (1996) Complete sequence analysis of the genome of the bacterium Mycoplasma pneumoniae. Nucleic Acids Res. 24, 4420-4449.
201. Blattner, F.R. et al. (1997) The complete genome sequence of Escherichia coli K-12. Science 277, 1453-1474.
202. Smith, D.R. et al. (1997) Complete genome sequence of Methanobacterium thermoautotrophicum deltaH: functional analysis and comparative genomics. J. Bacteriol. 179, 7135-7155.
203. Kunst, F. et al. (1997) The complete genome sequence of the gram-positive bacterium Bacillus subtilis. Nature 390, 249-256.
204. Klenk, H.P. et al. (1997) The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus. Nature 390, 364-370.
205. Deckert, G. et al. (1998) The complete genome of the hyperthermophilic bacterium Aquifex aeolicus. Nature 392, 353-358.
206. Kraulis, P.J. (1991) MOLSCRIPT - a program to produce both detailed and schematic plots of protein structures. J. Appl. Cryst. 24, 946-950.
207. Wootton, J.C. and Federhen, S. (1996) Analysis of compositionally biased regions in sequence databases. Methods Enzymol. 266, 554-571.
208. Wootton, J.C. (1994) Non-globular domains in protein sequences: automated segmentation using complexity measures. Comput. Chem. 18, 269-285.