-
1
-
-
0028961335
-
SCOP: a structural classification of proteins database for the investigation of sequences and structures
-
Murzin AG, Brenner SE, Hubbard T, Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 1995; 247: 536-540.
-
(1995)
J. Mol. Biol.
, vol.247
, pp. 536-540
-
-
Murzin, A.G.1
Brenner, S.E.2
Hubbard, T.3
Chothia, C.4
-
2
-
-
0041317258
-
More than the sum of their parts: on the evolution of proteins from peptides
-
Söding J, Lupas AN. More than the sum of their parts: on the evolution of proteins from peptides. Bioessays 2003; 25: 837-846.
-
(2003)
Bioessays
, vol.25
, pp. 837-846
-
-
Söding, J.1
Lupas, A.N.2
-
3
-
-
34247131307
-
Enzyme promiscuity: mechanism and applications
-
Hult K, Berglund P. Enzyme promiscuity: mechanism and applications. Trends Biotechnol. 2007; 25: 231238.
-
(2007)
Trends Biotechnol.
, vol.25
, pp. 231238
-
-
Hult, K.1
Berglund, P.2
-
5
-
-
0034682335
-
Lateral gene transfer and the nature of bacterial innovation
-
Ochman H, Lawrence JG, Groisman EA. Lateral gene transfer and the nature of bacterial innovation. Nature 2000; 405: 299-304.
-
(2000)
Nature
, vol.405
, pp. 299-304
-
-
Ochman, H.1
Lawrence, J.G.2
Groisman, E.A.3
-
6
-
-
0032193729
-
Evolution of the structure and chromosomal distribution of histidine biosynthetic genes
-
Fani R, Mori E, Tamburini E, Lazcano A. Evolution of the structure and chromosomal distribution of histidine biosynthetic genes. Orig Life Evol Biosph 1998; 28: 555-570.
-
(1998)
Orig Life Evol Biosph
, vol.28
, pp. 555-570
-
-
Fani, R.1
Mori, E.2
Tamburini, E.3
Lazcano, A.4
-
7
-
-
0034634395
-
The evolutionary fate and consequences of duplicate genes
-
Lynch M, Conery JS. The evolutionary fate and consequences of duplicate genes. Science 2000; 290: 1151-1155.
-
(2000)
Science
, vol.290
, pp. 1151-1155
-
-
Lynch, M.1
Conery, J.S.2
-
8
-
-
33646572856
-
Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. What is the role of genome duplication in the evolution of complexity and diversity?
-
Crow KD, Wagner GP. Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. What is the role of genome duplication in the evolution of complexity and diversity? Mol. Biol. Evol. 2006; 23: 887-892.
-
(2006)
Mol. Biol. Evol.
, vol.23
, pp. 887-892
-
-
Crow, K.D.1
Wagner, G.P.2
-
9
-
-
0031974376
-
The evolutionary relationships between the two bacteria Escherichia coli and Haemophilus influenzae and their putative last common ancestor
-
de Rosa R, Labedan B. The evolutionary relationships between the two bacteria Escherichia coli and Haemophilus influenzae and their putative last common ancestor. Mol. Biol. Evol. 1998; 15: 17-27.
-
(1998)
Mol. Biol. Evol.
, vol.15
, pp. 17-27
-
-
de Rosa, R.1
Labedan, B.2
-
10
-
-
70349979682
-
Origin and evolution of operons and metabolic pathways
-
Fondi M, Emiliani G, Fani R. Origin and evolution of operons and metabolic pathways. Res. Microbiol. 2009; 160: 502-512.
-
(2009)
Res. Microbiol.
, vol.160
, pp. 502-512
-
-
Fondi, M.1
Emiliani, G.2
Fani, R.3
-
11
-
-
0028918594
-
Engineering the stability and function of gene V protein
-
Terwilliger TC. Engineering the stability and function of gene V protein. Adv. Protein Chem. 1995; 46: 177-215.
-
(1995)
Adv. Protein Chem.
, vol.46
, pp. 177-215
-
-
Terwilliger, T.C.1
-
12
-
-
0030623398
-
An inverse correlation between loop length and stability in a four-helix-bundle protein
-
Nagi AD, Regan L. An inverse correlation between loop length and stability in a four-helix-bundle protein. Fold Des. 1997; 2: 67-75.
-
(1997)
Fold Des.
, vol.2
, pp. 67-75
-
-
Nagi, A.D.1
Regan, L.2
-
13
-
-
0024511257
-
Co-operativity in protein-protein association. The structure and stability of the actin filament
-
Erickson HP. Co-operativity in protein-protein association. The structure and stability of the actin filament. J. Mol. Biol. 1989; 206: 465-474.
-
(1989)
J. Mol. Biol.
, vol.206
, pp. 465-474
-
-
Erickson, H.P.1
-
15
-
-
0033618555
-
Detecting protein function and protein-protein interactions from genome sequences
-
Marcotte EM, Pellegrini M, Ng HL, Rice DW, Yeates TO, Eisenberg D. Detecting protein function and protein-protein interactions from genome sequences. Science 1999; 285: 751-753.
-
(1999)
Science
, vol.285
, pp. 751-753
-
-
Marcotte, E.M.1
Pellegrini, M.2
Ng, H.L.3
Rice, D.W.4
Yeates, T.O.5
Eisenberg, D.6
-
16
-
-
41149106300
-
Evolution of the beta-propeller fold
-
Chaudhuri I, Soding J, Lupas AN. Evolution of the beta-propeller fold. Proteins 2008; 71: 795-803.
-
(2008)
Proteins
, vol.71
, pp. 795-803
-
-
Chaudhuri, I.1
Soding, J.2
Lupas, A.N.3
-
17
-
-
0034284955
-
Structural evidence for evolution of the beta/alpha barrel scaffold by gene duplication and fusion
-
Lang D, Thoma R, Henn-Sax M, Sterner R, Wilmanns M. Structural evidence for evolution of the beta/alpha barrel scaffold by gene duplication and fusion. Science 2000; 289: 1546-1550.
-
(2000)
Science
, vol.289
, pp. 1546-1550
-
-
Lang, D.1
Thoma, R.2
Henn-Sax, M.3
Sterner, R.4
Wilmanns, M.5
-
18
-
-
0034746909
-
Dissection of a (betaalpha)8-barrel enzyme into two folded halves
-
Höcker B, Beismann-Driemeyer S, Hettwer S, Lustig A, Sterner R. Dissection of a (betaalpha)8-barrel enzyme into two folded halves. Nat. Struct. Biol. 2001; 8: 32-36.
-
(2001)
Nat. Struct. Biol.
, vol.8
, pp. 32-36
-
-
Höcker, B.1
Beismann-Driemeyer, S.2
Hettwer, S.3
Lustig, A.4
Sterner, R.5
-
19
-
-
9344235017
-
Mimicking enzyme evolution by generating new (betaalpha)8-barrels from (betaalpha)4-half-barrels
-
Höcker B, Claren J, Sterner R. Mimicking enzyme evolution by generating new (betaalpha)8-barrels from (betaalpha)4-half-barrels. Proc. Natl. Acad. Sci. U. S. A. 2004; 101: 16448-16453.
-
(2004)
Proc. Natl. Acad. Sci. U. S. A.
, vol.101
, pp. 16448-16453
-
-
Höcker, B.1
Claren, J.2
Sterner, R.3
-
20
-
-
34547662332
-
Stabilisation of a (betaalpha)8-barrel protein designed from identical half barrels
-
Seitz T, Bocola M, Claren J, Sterner R. Stabilisation of a (betaalpha)8-barrel protein designed from identical half barrels. J. Mol. Biol. 2007; 372: 114-129.
-
(2007)
J. Mol. Biol.
, vol.372
, pp. 114-129
-
-
Seitz, T.1
Bocola, M.2
Claren, J.3
Sterner, R.4
-
21
-
-
64349124286
-
High-resolution crystal structure of an artificial (betaalpha)(8)-barrel protein designed from identical half-barrels
-
Höcker B, Lochner A, Seitz T, Claren J, Sterner R. High-resolution crystal structure of an artificial (betaalpha)(8)-barrel protein designed from identical half-barrels. Biochemistry 2009; 48: 1145-1147.
-
(2009)
Biochemistry
, vol.48
, pp. 1145-1147
-
-
Höcker, B.1
Lochner, A.2
Seitz, T.3
Claren, J.4
Sterner, R.5
-
22
-
-
0037452697
-
Designed to be stable: crystal structure of a consensus ankyrin repeat protein
-
Kohl A, Binz HK, Forrer P, Stumpp MT, Plückthun A, Grutter MG. Designed to be stable: crystal structure of a consensus ankyrin repeat protein. Proc. Natl. Acad. Sci. U. S. A. 2003; 100: 1700-1705.
-
(2003)
Proc. Natl. Acad. Sci. U. S. A.
, vol.100
, pp. 1700-1705
-
-
Kohl, A.1
Binz, H.K.2
Forrer, P.3
Stumpp, M.T.4
Plückthun, A.5
Grutter, M.G.6
-
24
-
-
0037648552
-
Design of stable alpha-helical arrays from an idealized TPR motif
-
Main ER, Xiong Y, Cocco MJ, D'Andrea L, Regan L. Design of stable alpha-helical arrays from an idealized TPR motif. Structure 2003; 11: 497-508.
-
(2003)
Structure
, vol.11
, pp. 497-508
-
-
Main, E.R.1
Xiong, Y.2
Cocco, M.J.3
D'Andrea, L.4
Regan, L.5
-
25
-
-
0043281585
-
Designing repeat proteins: modular leucine-rich repeat protein libraries based on the mammalian ribonuclease inhibitor family
-
Stumpp MT, Forrer P, Binz HK, Plückthun A. Designing repeat proteins: modular leucine-rich repeat protein libraries based on the mammalian ribonuclease inhibitor family. J. Mol. Biol. 2003; 332: 471-487.
-
(2003)
J. Mol. Biol.
, vol.332
, pp. 471-487
-
-
Stumpp, M.T.1
Forrer, P.2
Binz, H.K.3
Plückthun, A.4
-
26
-
-
39149098445
-
Designed armadillo repeat proteins as general peptide-binding scaffolds: consensus design and computational optimization of the hydrophobic core
-
Parmeggiani F, Pellarin R, Larsen AP, Varadamsetty G, Stumpp MT, Zerbe O, Caflisch A, Plückthun A. Designed armadillo repeat proteins as general peptide-binding scaffolds: consensus design and computational optimization of the hydrophobic core. J. Mol. Biol. 2008; 376: 1282-1304.
-
(2008)
J. Mol. Biol.
, vol.376
, pp. 1282-1304
-
-
Parmeggiani, F.1
Pellarin, R.2
Larsen, A.P.3
Varadamsetty, G.4
Stumpp, M.T.5
Zerbe, O.6
Caflisch, A.7
Plückthun, A.8
-
27
-
-
2342624119
-
High-affinity binders selected from designed ankyrin repeat protein libraries
-
Binz HK, Amstutz P, Kohl A, Stumpp MT, Briand C, Forrer P, Grütter MG, Plückthun A. High-affinity binders selected from designed ankyrin repeat protein libraries. Nat. Biotechnol. 2004; 22: 575-582.
-
(2004)
Nat. Biotechnol.
, vol.22
, pp. 575-582
-
-
Binz, H.K.1
Amstutz, P.2
Kohl, A.3
Stumpp, M.T.4
Briand, C.5
Forrer, P.6
Grütter, M.G.7
Plückthun, A.8
-
28
-
-
27144511241
-
Engineering novel binding proteins from nonimmunoglobulin domains
-
Binz HK, Amstutz P, Plückthun A. Engineering novel binding proteins from nonimmunoglobulin domains. Nat. Biotechnol. 2005; 23: 1257-1268.
-
(2005)
Nat. Biotechnol.
, vol.23
, pp. 1257-1268
-
-
Binz, H.K.1
Amstutz, P.2
Plückthun, A.3
-
29
-
-
37249046360
-
Finding a match: how do homologous sequences get together for recombination?
-
Barzel A, Kupiec M. Finding a match: how do homologous sequences get together for recombination? Nat. Rev. 2008; 9: 27-37.
-
(2008)
Nat. Rev.
, vol.9
, pp. 27-37
-
-
Barzel, A.1
Kupiec, M.2
-
30
-
-
0037031655
-
Identification of a DNA nonhomologous end-joining complex in bacteria
-
Weller GR, Kysela B, Roy R, Tonkin LM, Scalan E, Della M, Devine SK, Day JP, Wilkinson A, d'Adda di Fagagna F, Devine KM, Bowater RP, Jeggo PA, Jackson SP, Doherty AJ. Identification of a DNA nonhomologous end-joining complex in bacteria. Science 2002; 297: 1686-1689.
-
(2002)
Science
, vol.297
, pp. 1686-1689
-
-
Weller, G.R.1
Kysela, B.2
Roy, R.3
Tonkin, L.M.4
Scalan, E.5
Della, M.6
Devine, S.K.7
Day, J.P.8
Wilkinson, A.9
d'Adda di Fagagna, F.10
Devine, K.M.11
Bowater, R.P.12
Jeggo, P.A.13
Jackson, S.P.14
Doherty, A.J.15
-
32
-
-
23944454205
-
Generating molecular diversity by homologous recombination in Escherichia coli
-
Wang PL, Lo BK, Winter G. Generating molecular diversity by homologous recombination in Escherichia coli. Protein Eng. Des. Sel. 2005; 18: 397-404.
-
(2005)
Protein Eng. Des. Sel.
, vol.18
, pp. 397-404
-
-
Wang, P.L.1
Lo, B.K.2
Winter, G.3
-
34
-
-
0034730144
-
Novel folded protein domains generated by combinatorial shuffling of polypeptide segments
-
Riechmann L, Winter G. Novel folded protein domains generated by combinatorial shuffling of polypeptide segments. Proc. Natl. Acad. Sci. U. S. A. 2000; 97: 10068-10073.
-
(2000)
Proc. Natl. Acad. Sci. U. S. A.
, vol.97
, pp. 10068-10073
-
-
Riechmann, L.1
Winter, G.2
-
35
-
-
33748939410
-
Early protein evolution: building domains from ligand-binding polypeptide segments
-
Riechmann L, Winter G. Early protein evolution: building domains from ligand-binding polypeptide segments. J. Mol. Biol. 2006; 363: 460-468.
-
(2006)
J. Mol. Biol.
, vol.363
, pp. 460-468
-
-
Riechmann, L.1
Winter, G.2
-
36
-
-
62649123200
-
Establishing wild-type levels of catalytic activity on natural and artificial (beta alpha)8-barrel protein scaffolds
-
Claren J, Malisi C, Höcker B, Sterner R. Establishing wild-type levels of catalytic activity on natural and artificial (beta alpha)8-barrel protein scaffolds. Proc. Natl. Acad. Sci. U. S. A. 2009; 106: 3704-3709.
-
(2009)
Proc. Natl. Acad. Sci. U. S. A.
, vol.106
, pp. 3704-3709
-
-
Claren, J.1
Malisi, C.2
Höcker, B.3
Sterner, R.4
-
37
-
-
0037116603
-
A common evolutionary origin of two elementary enzyme folds
-
Höcker B, Schmidt S, Sterner R. A common evolutionary origin of two elementary enzyme folds. FEBS Lett. 2002; 510: 133-135.
-
(2002)
FEBS Lett.
, vol.510
, pp. 133-135
-
-
Höcker, B.1
Schmidt, S.2
Sterner, R.3
-
39
-
-
0032518266
-
DNA shuffling of a family of genes from diverse species accelerates directed evolution
-
Crameri A, Raillard SA, Bermudez E, Stemmer WP. DNA shuffling of a family of genes from diverse species accelerates directed evolution. Nature 1998; 391: 288-291.
-
(1998)
Nature
, vol.391
, pp. 288-291
-
-
Crameri, A.1
Raillard, S.A.2
Bermudez, E.3
Stemmer, W.P.4
-
40
-
-
0032866310
-
Evolution of a cytokine using DNA family shuffling
-
Chang CC, Chen TT, Cox BW, Dawes GN, Stemmer WP, Punnonen J, Patten PA. Evolution of a cytokine using DNA family shuffling. Nat. Biotechnol. 1999; 17: 793-797.
-
(1999)
Nat. Biotechnol.
, vol.17
, pp. 793-797
-
-
Chang, C.C.1
Chen, T.T.2
Cox, B.W.3
Dawes, G.N.4
Stemmer, W.P.5
Punnonen, J.6
Patten, P.A.7
-
41
-
-
0036606766
-
eCodonOpt: a systematic computational framework for optimizing codon usage in directed evolution experiments
-
Moore GL, Maranas CD. eCodonOpt: a systematic computational framework for optimizing codon usage in directed evolution experiments. Nucleic Acids Res. 2002; 30: 2407-2416.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 2407-2416
-
-
Moore, G.L.1
Maranas, C.D.2
-
42
-
-
17444363724
-
A combinatorial approach to hybrid enzymes independent of DNA homology
-
Ostermeier M, Shim JH, Benkovic SJ. A combinatorial approach to hybrid enzymes independent of DNA homology. Nat. Biotechnol. 1999; 17: 1205-1209.
-
(1999)
Nat. Biotechnol.
, vol.17
, pp. 1205-1209
-
-
Ostermeier, M.1
Shim, J.H.2
Benkovic, S.J.3
-
43
-
-
3042739160
-
The creation of ITCHY hybrid protein libraries
-
Ostermeier M, Lutz S. The creation of ITCHY hybrid protein libraries. Methods Mol. Biol. 2003; 231: 129-141.
-
(2003)
Methods Mol. Biol.
, vol.231
, pp. 129-141
-
-
Ostermeier, M.1
Lutz, S.2
-
44
-
-
0034842485
-
Circularly permuted proteins in the protein structure database
-
Jung J, Lee B. Circularly permuted proteins in the protein structure database. Protein Sci. 2001; 10: 1881-1886.
-
(2001)
Protein Sci.
, vol.10
, pp. 1881-1886
-
-
Jung, J.1
Lee, B.2
-
46
-
-
33750016048
-
Duplication, divergence and formation of novel protein topologies
-
Vogel C, Morea V. Duplication, divergence and formation of novel protein topologies. Bioessays 2006; 28: 973-978.
-
(2006)
Bioessays
, vol.28
, pp. 973-978
-
-
Vogel, C.1
Morea, V.2
-
47
-
-
0022001083
-
Polypeptide ligation occurs during post-translational modification of concanavalin A
-
Carrington DM, Auffret A, Hanke DE. Polypeptide ligation occurs during post-translational modification of concanavalin A. Nature 1985; 313: 64-67.
-
(1985)
Nature
, vol.313
, pp. 64-67
-
-
Carrington, D.M.1
Auffret, A.2
Hanke, D.E.3
-
48
-
-
31744450975
-
Evolution of new protein topologies through multistep gene rearrangements
-
Peisajovich SG, Rockah L, Tawfik DS. Evolution of new protein topologies through multistep gene rearrangements. Nat. Genet. 2006; 38: 168-174.
-
(2006)
Nat. Genet.
, vol.38
, pp. 168-174
-
-
Peisajovich, S.G.1
Rockah, L.2
Tawfik, D.S.3
-
49
-
-
44949143819
-
Cradle-loop barrels and the concept of metafolds in protein classification by natural descent
-
Alva V, Koretke KK, Coles M, Lupas AN. Cradle-loop barrels and the concept of metafolds in protein classification by natural descent. Curr. Opin. Struct. Biol. 2008; 18: 358-365.
-
(2008)
Curr. Opin. Struct. Biol.
, vol.18
, pp. 358-365
-
-
Alva, V.1
Koretke, K.K.2
Coles, M.3
Lupas, A.N.4
-
50
-
-
0024490818
-
Correct folding of circularly permuted variants of a beta alpha barrel enzyme in vivo
-
Luger K, Hommel U, Herold M, Hofsteenge J, Kirschner K. Correct folding of circularly permuted variants of a beta alpha barrel enzyme in vivo. Science 1989; 243: 206-210.
-
(1989)
Science
, vol.243
, pp. 206-210
-
-
Luger, K.1
Hommel, U.2
Herold, M.3
Hofsteenge, J.4
Kirschner, K.5
-
51
-
-
0029859408
-
Random circular permutation of genes and expressed polypeptide chains: application of the method to the catalytic chains of aspartate transcarbamoylase
-
Graf R, Schachman HK. Random circular permutation of genes and expressed polypeptide chains: application of the method to the catalytic chains of aspartate transcarbamoylase. Proc. Natl. Acad. Sci. U. S. A. 1996; 93: 11591-11596.
-
(1996)
Proc. Natl. Acad. Sci. U. S. A.
, vol.93
, pp. 11591-11596
-
-
Graf, R.1
Schachman, H.K.2
-
52
-
-
23844465160
-
Directed evolution of protein switches and their application to the creation of ligand-binding proteins
-
Guntas G, Mansell TJ, Kim JR, Ostermeier M. Directed evolution of protein switches and their application to the creation of ligand-binding proteins. Proc. Natl. Acad. Sci. U. S. A. 2005; 102: 11224-11229.
-
(2005)
Proc. Natl. Acad. Sci. U. S. A.
, vol.102
, pp. 11224-11229
-
-
Guntas, G.1
Mansell, T.J.2
Kim, J.R.3
Ostermeier, M.4
-
53
-
-
0346500466
-
Creation of an allosteric enzyme by domain insertion
-
Guntas G, Ostermeier M. Creation of an allosteric enzyme by domain insertion. J. Mol. Biol. 2004; 336: 263-273.
-
(2004)
J. Mol. Biol.
, vol.336
, pp. 263-273
-
-
Guntas, G.1
Ostermeier, M.2
-
54
-
-
0033923044
-
Systematic circular permutation of an entire protein reveals essential folding elements
-
Iwakura M, Nakamura T, Yamane C, Maki K. Systematic circular permutation of an entire protein reveals essential folding elements. Nat. Struct. Biol. 2000; 7: 580-585.
-
(2000)
Nat. Struct. Biol.
, vol.7
, pp. 580-585
-
-
Iwakura, M.1
Nakamura, T.2
Yamane, C.3
Maki, K.4
-
55
-
-
70349255505
-
Structural redesign of lipase B from Candida antarctica by circular permutation and incremental truncation
-
Qian Z, Horton JR, Cheng X, Lutz S. Structural redesign of lipase B from Candida antarctica by circular permutation and incremental truncation. J. Mol. Biol. 2009; 393: 191-201.
-
(2009)
J. Mol. Biol.
, vol.393
, pp. 191-201
-
-
Qian, Z.1
Horton, J.R.2
Cheng, X.3
Lutz, S.4
-
56
-
-
78149378424
-
Tying up the loose ends: circular permutation decreases the proteolytic susceptibility of recombinant proteins
-
Whitehead TA, Bergeron LM, Clark DS. Tying up the loose ends: circular permutation decreases the proteolytic susceptibility of recombinant proteins. Protein Eng. Des. Sel. 2009; 22: 607-613.
-
(2009)
Protein Eng. Des. Sel.
, vol.22
, pp. 607-613
-
-
Whitehead, T.A.1
Bergeron, L.M.2
Clark, D.S.3
-
57
-
-
4644349676
-
Circular permutation as a tool to reduce surface entropy triggers crystallization of the signal recognition particle receptor beta subunit
-
Schwartz TU, Walczak R, Blobel G. Circular permutation as a tool to reduce surface entropy triggers crystallization of the signal recognition particle receptor beta subunit. Protein Sci. 2004; 13: 2814-2818.
-
(2004)
Protein Sci.
, vol.13
, pp. 2814-2818
-
-
Schwartz, T.U.1
Walczak, R.2
Blobel, G.3
-
58
-
-
33845475425
-
Immunogenicity of a Yersinia pestis vaccine antigen monomerized by circular permutation
-
Chalton DA, Musson JA, Flick-Smith H, Walker N, McGregor A, Lamb HK, Williamson ED, Miller J, Robinson JH, Lakey JH. Immunogenicity of a Yersinia pestis vaccine antigen monomerized by circular permutation. Infect. Immun. 2006; 74: 6624-6631.
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(2006)
Infect. Immun.
, vol.74
, pp. 6624-6631
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Chalton, D.A.1
Musson, J.A.2
Flick-Smith, H.3
Walker, N.4
McGregor, A.5
Lamb, H.K.6
Williamson, E.D.7
Miller, J.8
Robinson, J.H.9
Lakey, J.H.10
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