-
1
-
-
0003880161
-
-
Garland, New York, ed. 3
-
B. Alberts et al., Molecular Biology of the Cell (Garland, New York, ed. 3, 1994); H. Lodish et al., Molecular Cell Biology (Scientific American Books, New York, ed. 3, 1995).
-
(1994)
Molecular Biology of the Cell
-
-
Alberts, B.1
-
2
-
-
0003422388
-
-
Scientific American Books, New York, ed. 3
-
B. Alberts et al., Molecular Biology of the Cell (Garland, New York, ed. 3, 1994); H. Lodish et al., Molecular Cell Biology (Scientific American Books, New York, ed. 3, 1995).
-
(1995)
Molecular Cell Biology
-
-
Lodish, H.1
-
4
-
-
0030045003
-
-
J. M. Berger, S. J. Gamblin, S. C. Harrison, J. C. Wang, Ibid. 379, 225 (1996).
-
(1996)
Nature
, vol.379
, pp. 225
-
-
Berger, J.M.1
Gamblin, S.J.2
Harrison, S.C.3
Wang, J.C.4
-
5
-
-
15444350252
-
-
F. R. Blattner et al., Science 277, 1453 (1997).
-
(1997)
Science
, vol.277
, pp. 1453
-
-
Blattner, F.R.1
-
6
-
-
0345583058
-
-
The triplets of proteins are found with the aid of protein domain databases such as the ProDom or Pfam databases (17). Here, a list of all ProDom domains in every one of the 64,568 SWISS-PROT proteins was prepared, as well as a list of all proteins that contain each of the 53,597 ProDom domains. Then every protein in ProDom was considered for its ability to be a linking (or Rosetta Stone) member in a triplet. All pairs of domains that are both members of a given protein P were defined as being linked by protein P, if we could find at least one protein with only one of the two domains. By this method, we found 14,899 links between the 7843 ProDom domains. Then in a single genome (such as E. coli), we found all nonhomologous pairs of proteins containing linked domains. These pairs are linked by the Rosetta Stone proteins. For E. coli, this method finds 3531 protein pairs. An alternate method for discovering protein triplets uses amino acid sequence alignment techniques to find two proteins that align to a Rosetta Stone protein such that the alignments do not overlap on the Rosetta Stone protein. For E. coli, this method finds 4487 protein pairs, 1209 of which were also found by the ProDom search method (even though different sequence databases were searched for each method). All predictions are available on the World Wide Web at www.doe-mbi.ucla.edu.
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7
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0345151209
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note
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Two amino acid sequences are said to be similar when the sequences align with a statistically significant alignment score. The significance is described by the probability of obtaining a higher alignment score when comparing shuffled sequences, with the acceptable probability threshold set by considering the total number of sequence comparisons performed. That is, if n proteins in E. coli are compared with m proteins in other genomes, n X m total comparisons are performed. We set a probability of 1/(n X m) as the threshold as this is the lowest value that could be obtained by comparing n X m random sequences. For the ProDom-based identification of homologs, definitions of sequence similarity are as in the ProDom database.
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8
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0345150848
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The SWISS-PROT database is available at www. expasy.ch/sprot/.
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9
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0345151206
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The Database of Interacting Proteins is available on the Web at http://www.doe-mbi.ucla.edu.
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10
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0033551248
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-
M. Pellegrini, E. M. Marcotte, M. J. Thompson, D. Eisenberg, T. O. Yeates, Proc. Natl. Acad. Sci. U.S.A. 96, 4285 (1999).
-
(1999)
Proc. Natl. Acad. Sci. U.S.A.
, vol.96
, pp. 4285
-
-
Pellegrini, M.1
Marcotte, E.M.2
Thompson, M.J.3
Eisenberg, D.4
Yeates, T.O.5
-
11
-
-
0024511257
-
-
H. P. Erickson, J. Mol. Biol. 206, 465 (1989); A. D. Nagi and L. Regan, Folding Design 2, 67 (1997).
-
(1989)
J. Mol. Biol.
, vol.206
, pp. 465
-
-
Erickson, H.P.1
-
13
-
-
0017861127
-
-
S. Pederson, P. S. Bloch, S. Reen, F. C. Neidhardt, Cell 14, 179 (1978).
-
(1978)
Cell
, vol.14
, pp. 179
-
-
Pederson, S.1
Bloch, P.S.2
Reen, S.3
Neidhardt, F.C.4
-
16
-
-
0028853544
-
-
N. Horton and M. Lewis, Protein Sci. 1, 169 (1992); J. Janin, Biochimie 77, 497 (1995).
-
(1995)
Biochimie
, vol.77
, pp. 497
-
-
Janin, J.1
-
18
-
-
0031025991
-
-
W. Xu, S. C. Harrison, M. J. Eck, Nature 385, 595 (1997); F. Sicheri, I. Moarefi, J. Kuriyan, ibid., p. 602.
-
(1997)
Nature
, vol.385
, pp. 595
-
-
Xu, W.1
Harrison, S.C.2
Eck, M.J.3
-
19
-
-
0031034930
-
-
W. Xu, S. C. Harrison, M. J. Eck, Nature 385, 595 (1997); F. Sicheri, I. Moarefi, J. Kuriyan, ibid., p. 602.
-
Nature
, pp. 602
-
-
Sicheri, F.1
Moarefi, I.2
Kuriyan, J.3
-
20
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0345151196
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note
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The error in predicting protein-protein interactions due to the inability to distinguish homologs was estimated as 1-T, where T is the mean percentage of potential true positives calculated for all domain pairs in E. coli. For each domain pair linked by a Rosetta Stone protein, there are n proteins with the first domain but not the second and m proteins with the second domain but not the first The percentage of true positives T is therefore estimated as the smaller of n or m divided by n times m.
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21
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0031812904
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F. Corpet, J. Gouzy, D. Kahn, Nucleic Acids Res. 26, 323 (1998); A. Bateman et al., ibid. 27, 260 (1999).
-
(1998)
Nucleic Acids Res.
, vol.26
, pp. 323
-
-
Corpet, F.1
Gouzy, J.2
Kahn, D.3
-
22
-
-
0032952229
-
-
F. Corpet, J. Gouzy, D. Kahn, Nucleic Acids Res. 26, 323 (1998); A. Bateman et al., ibid. 27, 260 (1999).
-
(1999)
Nucleic Acids Res.
, vol.27
, pp. 260
-
-
Bateman, A.1
-
23
-
-
0019322527
-
-
A. Sugino, N. P. Higgins, N. R. Cozzarelli, ibid. 8, 3865 (1980); W. K. Yeh and L. N. Omston, J. Biol. Chem. 256, 1565 (1981); C. S. McHenry and W. Crow, ibid. 254, 1748 (1979).
-
(1980)
Nucleic Acids Res.
, vol.8
, pp. 3865
-
-
Sugino, A.1
Higgins, N.P.2
Cozzarelli, N.R.3
-
24
-
-
0019405352
-
-
A. Sugino, N. P. Higgins, N. R. Cozzarelli, ibid. 8, 3865 (1980); W. K. Yeh and L. N. Omston, J. Biol. Chem. 256, 1565 (1981); C. S. McHenry and W. Crow, ibid. 254, 1748 (1979).
-
(1981)
J. Biol. Chem.
, vol.256
, pp. 1565
-
-
Yeh, W.K.1
Omston, L.N.2
-
25
-
-
0018786252
-
-
A. Sugino, N. P. Higgins, N. R. Cozzarelli, ibid. 8, 3865 (1980); W. K. Yeh and L. N. Omston, J. Biol. Chem. 256, 1565 (1981); C. S. McHenry and W. Crow, ibid. 254, 1748 (1979).
-
(1979)
J. Biol. Chem.
, vol.254
, pp. 1748
-
-
McHenry, C.S.1
Crow, W.2
-
26
-
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0019443447
-
-
Table II
-
See Table II of J. S. Richardson, Adv. Protein Chem. 34, 167 (1981). Note also that eukaryotic genes, in contrast to prokaryotic genes, often code for multidomain proteins [W. J. Netzer and F. U. Hartl, Nature 388, 343 (1997)].
-
(1981)
Adv. Protein Chem.
, vol.34
, pp. 167
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-
Richardson, J.S.1
-
27
-
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0030844281
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See Table II of J. S. Richardson, Adv. Protein Chem. 34, 167 (1981). Note also that eukaryotic genes, in contrast to prokaryotic genes, often code for multidomain proteins [W. J. Netzer and F. U. Hartl, Nature 388, 343 (1997)].
-
(1997)
Nature
, vol.388
, pp. 343
-
-
Netzer, W.J.1
Hartl, F.U.2
-
29
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0344288906
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note
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Supported by the following grants: Department of Energy (DOE) DE-FC03-87ER-60615, NIH PO1 GM 31299, and NSF MCB 94 20769. E. M. was supported by a DOE Hollaender fellowship. We thank M. K. Baron for her work with the Database of Interacting Proteins.
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