-
1
-
-
70350482286
-
Evolution of biomolecular networks: Lessons from metabolic and protein interactions
-
Yamada T, Bork P (2009) Evolution of biomolecular networks: lessons from metabolic and protein interactions. Nat Rev Mol Cell Biol 10: 791-803.
-
(2009)
Nat Rev Mol Cell Biol
, vol.10
, pp. 791-803
-
-
Yamada, T.1
Bork, P.2
-
2
-
-
12444301754
-
Structure and evolution of protein interaction networks: A statistical model for link dynamics and gene duplications
-
Berg J, Lassig M, Wagner A (2004) Structure and evolution of protein interaction networks: a statistical model for link dynamics and gene duplications. BMC Evol Biol 4: 51.
-
(2004)
BMC Evol Biol
, vol.4
, pp. 51
-
-
Berg, J.1
Lassig, M.2
Wagner, A.3
-
3
-
-
44949142848
-
Evolution and dynamics of protein interactions and networks
-
Levy ED, Pereira-Leal JB (2008) Evolution and dynamics of protein interactions and networks. Curr Opin Struct Biol 18: 349-357.
-
(2008)
Curr Opin Struct Biol
, vol.18
, pp. 349-357
-
-
Levy, E.D.1
Pereira-Leal, J.B.2
-
4
-
-
0037423828
-
How the global structure of protein interaction networks evolves
-
Wagner A (2003) How the global structure of protein interaction networks evolves. Proc Biol Sci 270: 457-466.
-
(2003)
Proc Biol Sci
, vol.270
, pp. 457-466
-
-
Wagner, A.1
-
5
-
-
33845875196
-
Relating three-dimensional structures to protein networks provides evolutionary insights
-
DOI 10.1126/science.1136174
-
Kim PM, Lu LJ, Xia Y, Gerstein MB (2006) Relating three-dimensional structures to protein networks provides evolutionary insights. Science 314: 1938-1941. (Pubitemid 46026118)
-
(2006)
Science
, vol.314
, Issue.5807
, pp. 1938-1941
-
-
Kim, P.M.1
Lu, L.J.2
Xia, Y.3
Gerstein, M.B.4
-
6
-
-
4644292576
-
The yeast coexpression network has a small-world, scale-free architecture and can be explained by a simple model
-
DOI 10.1038/sj.embor.7400090
-
van Noort V, Snel B, Huynen MA (2004) The yeast coexpression network has a small-world, scale-free architecture and can be explained by a simple model. EMBO Rep 5: 280-284. (Pubitemid 38500108)
-
(2004)
EMBO Reports
, vol.5
, Issue.3
, pp. 280-284
-
-
Van Noort, V.1
Snel, B.2
Huynen, M.A.3
-
7
-
-
27144511241
-
Engineering novel binding proteins from nonimmunoglobulin domains
-
DOI 10.1038/nbt1127, PII N1127
-
Binz HK, Amstutz P, Pluckthun A (2005) Engineering novel binding proteins from nonimmunoglobulin domains. Nat Biotechnol 23: 1257-1268. (Pubitemid 41486853)
-
(2005)
Nature Biotechnology
, vol.23
, Issue.10
, pp. 1257-1268
-
-
Binz, H.K.1
Amstutz, P.2
Pluckthun, A.3
-
8
-
-
34548522063
-
Alternative non-antibody scaffolds for molecular recognition
-
Skerra A (2007) Alternative non-antibody scaffolds for molecular recognition. Curr Opin Biotechnol 18: 295-304.
-
(2007)
Curr Opin Biotechnol
, vol.18
, pp. 295-304
-
-
Skerra, A.1
-
9
-
-
67649872364
-
Engineered protein scaffolds as next-generation antibody therapeutics
-
Gebauer M, Skerra A (2009) Engineered protein scaffolds as next-generation antibody therapeutics. Curr Opin Chem Biol 13: 245-255.
-
(2009)
Curr Opin Chem Biol
, vol.13
, pp. 245-255
-
-
Gebauer, M.1
Skerra, A.2
-
10
-
-
0032509129
-
The fibronectin type III domain as a scaffold for novel binding proteins
-
DOI 10.1006/jmbi.1998.2238
-
Koide A, Bailey CW, Huang X, Koide S (1998) The fibronectin type III domain as a scaffold for novel binding proteins. J Mol Biol 284: 1141-1151. (Pubitemid 28558562)
-
(1998)
Journal of Molecular Biology
, vol.284
, Issue.4
, pp. 1141-1151
-
-
Koide, A.1
Bailey, C.W.2
Huang, X.3
Koide, S.4
-
11
-
-
18544397601
-
Directed evolution of high-affinity antibody mimics using mRNA display
-
DOI 10.1016/S1074-5521(02)00187-4, PII S1074552102001874
-
Xu L, Aha P, Gu K, Kuimelis RG, Kurz M, et al. (2002) Directed evolution of high-affinity antibody mimics using mRNA display. Chem Biol 9: 933-942. (Pubitemid 35240913)
-
(2002)
Chemistry and Biology
, vol.9
, Issue.8
, pp. 933-942
-
-
Xu, L.1
Aha, P.2
Gu, K.3
Kuimelis, R.G.4
Kurz, M.5
Lam, T.6
Lim, A.C.7
Liu, H.8
Lohse, P.A.9
Sun, L.10
Weng, S.11
Wagner, R.W.12
Lipovsek, D.13
-
12
-
-
33646740974
-
Antagonists to Human and Mouse Vascular Endothelial Growth Factor Receptor 2 Generated by Directed Protein Evolution In Vitro
-
DOI 10.1016/j.chembiol.2005.12.009, PII S1074552106000081
-
Getmanova EV, Chen Y, Bloom L, Gokemeijer J, Shamah S, et al. (2006) Antagonists to human and mouse vascular endothelial growth factor receptor 2 generated by directed protein evolution in vitro. Chem Biol 13: 549-556. (Pubitemid 43744513)
-
(2006)
Chemistry and Biology
, vol.13
, Issue.5
, pp. 549-556
-
-
Getmanova, E.V.1
Chen, Y.2
Bloom, L.3
Gokemeijer, J.4
Shamah, S.5
Warikoo, V.6
Wang, J.7
Ling, V.8
Sun, L.9
-
13
-
-
79251508380
-
Phase I and pharmacokinetic study of CT-322 (BMS-844203), a targeted Adnectin inhibitor of VEGFR-2 based on a domain of human fibronectin
-
Tolcher AW, Sweeney CJ, Papadopoulos K, Patnaik A, Chiorean EG, et al. (2011) Phase I and pharmacokinetic study of CT-322 (BMS-844203), a targeted Adnectin inhibitor of VEGFR-2 based on a domain of human fibronectin. Clin Cancer Res 17: 363-371.
-
(2011)
Clin Cancer Res
, vol.17
, pp. 363-371
-
-
Tolcher, A.W.1
Sweeney, C.J.2
Papadopoulos, K.3
Patnaik, A.4
Chiorean, E.G.5
-
14
-
-
12844276589
-
Lipocalins in drug discovery: From natural ligand-binding proteins to 'anticalins'
-
DOI 10.1016/S1359-6446(04)03294-5, PII S1359644604032945
-
Schlehuber S, Skerra A (2005) Lipocalins in drug discovery: from natural ligand-binding proteins to ''anticalins''. Drug Discov Today 10: 23-33. (Pubitemid 40164816)
-
(2005)
Drug Discovery Today
, vol.10
, Issue.1
, pp. 23-33
-
-
Schlehuber, S.1
Skerra, A.2
-
15
-
-
27644540066
-
Anticalins as an alternative to antibody technology
-
DOI 10.1517/14712598.5.11.1453
-
Schlehuber S, Skerra A (2005) Anticalins as an alternative to antibody technology. Expert Opin Biol Ther 5: 1453-1462. (Pubitemid 41579430)
-
(2005)
Expert Opinion on Biological Therapy
, vol.5
, Issue.11
, pp. 1453-1462
-
-
Schlehuber, S.1
Skerra, A.2
-
16
-
-
34547911739
-
Anticalins as alternative binding proteins for therapeutic use
-
Skerra A (2007) Anticalins as alternative binding proteins for therapeutic use. Curr Opin Mol Ther 9: 336-344.
-
(2007)
Curr Opin Mol Ther
, vol.9
, pp. 336-344
-
-
Skerra, A.1
-
17
-
-
48149098354
-
DARPins: A new generation of protein therapeutics
-
Stumpp MT, Binz HK, Amstutz P (2008) DARPins: a new generation of protein therapeutics. Drug Discov Today 13: 695-701.
-
(2008)
Drug Discov Today
, vol.13
, pp. 695-701
-
-
Stumpp, M.T.1
Binz, H.K.2
Amstutz, P.3
-
19
-
-
2342624119
-
High-affinity binders selected from designed ankyrin repeat protein libraries
-
DOI 10.1038/nbt962
-
Binz HK, Amstutz P, Kohl A, Stumpp MT, Briand C, et al. (2004) High-affinity binders selected from designed ankyrin repeat protein libraries. Nat Biotechnol 22: 575-582. (Pubitemid 38590636)
-
(2004)
Nature Biotechnology
, vol.22
, Issue.5
, pp. 575-582
-
-
Binz, H.K.1
Amstutz, P.2
Kohl, A.3
Stumpp, M.T.4
Briand, C.5
Forrer, P.6
Grutter, M.G.7
Pluckthun, A.8
-
20
-
-
79956017135
-
Computational design of proteins targeting the conserved stem region of influenza hemagglutinin
-
Fleishman SJ, Whitehead TA, Ekiert DC, Dreyfus C, Corn JE, et al. (2011) Computational design of proteins targeting the conserved stem region of influenza hemagglutinin. Science 332: 816-821.
-
(2011)
Science
, vol.332
, pp. 816-821
-
-
Fleishman, S.J.1
Whitehead, T.A.2
Ekiert, D.C.3
Dreyfus, C.4
Corn, J.E.5
-
21
-
-
34447097241
-
Rational bases for the development of EGFR inhibitors for cancer treatment
-
DOI 10.1016/j.biocel.2007.05.008, PII S1357272507001495
-
Bianco R, Gelardi T, Damiano V, Ciardiello F, Tortora G (2007) Rational bases for the development of EGFR inhibitors for cancer treatment. Int J Biochem Cell Biol 39: 1416-1431. (Pubitemid 47031050)
-
(2007)
International Journal of Biochemistry and Cell Biology
, vol.39
, Issue.7-8
, pp. 1416-1431
-
-
Bianco, R.1
Gelardi, T.2
Damiano, V.3
Ciardiello, F.4
Tortora, G.5
-
22
-
-
23044502267
-
The epidermal growth factor receptor as a target for colorectal cancer therapy (vol 32, pg 52, 2005)
-
Lockhart AC (2005) The epidermal growth factor receptor as a target for colorectal cancer therapy (vol 32, pg 52, 2005). Seminars in Oncology 32: 432-432.
-
(2005)
Seminars in Oncology
, vol.32
, pp. 432-432
-
-
Lockhart, A.C.1
-
23
-
-
0034722889
-
The EGF receptor family as targets for cancer therapy
-
DOI 10.1038/sj.onc.1204082
-
Mendelsohn J, Baselga J (2000) The EGF receptor family as targets for cancer therapy. Oncogene 19: 6550-6565. (Pubitemid 32197693)
-
(2000)
Oncogene
, vol.19
, Issue.56
, pp. 6550-6565
-
-
Mendelsohn, J.1
Baselga, J.2
-
24
-
-
0033063774
-
The epidermal growth factor receptor and its inhibition in cancer therapy
-
Woodburn JR (1999) The epidermal growth factor receptor and its inhibition in cancer therapy. Pharmacol Ther 82: 241-250.
-
(1999)
Pharmacol Ther
, vol.82
, pp. 241-250
-
-
Woodburn, J.R.1
-
25
-
-
0037291769
-
EGF activates its receptor by removing interactions that autoinhibit ectodomain dimerization
-
DOI 10.1016/S1097-2765(03)00047-9
-
Ferguson KM, Berger MB, Mendrola JM, Cho HS, Leahy DJ, et al. (2003) EGF activates its receptor by removing interactions that autoinhibit ectodomain dimerization. Mol Cell 11: 507-517. (Pubitemid 36297057)
-
(2003)
Molecular Cell
, vol.11
, Issue.2
, pp. 507-517
-
-
Ferguson, K.M.1
Berger, M.B.2
Mendrola, J.M.3
Cho, H.-S.4
Leahy, D.J.5
Lemmon, M.A.6
-
26
-
-
18644386251
-
Crystal structure of the complex of human epidermal growth factor and receptor extracellular domains
-
DOI 10.1016/S0092-8674(02)00963-7
-
Ogiso H, Ishitani R, Nureki O, Fukai S, Yamanaka M, et al. (2002) Crystal structure of the complex of human epidermal growth factor and receptor extracellular domains. Cell 110: 775-787. (Pubitemid 35291060)
-
(2002)
Cell
, vol.110
, Issue.6
, pp. 775-787
-
-
Ogiso, H.1
Ishitani, R.2
Nureki, O.3
Fukai, S.4
Yamanaka, M.5
Kim, J.-H.6
Saito, K.7
Sakamoto, A.8
Inoue, M.9
Shirouzu, M.10
Yokoyama, S.11
-
27
-
-
17444403242
-
Structural basis for inhibition of the epidermal growth factor receptor by cetuximab
-
DOI 10.1016/j.ccr.2005.03.003
-
Li S, Schmitz KR, Jeffrey PD, Wiltzius JJ, Kussie P, et al. (2005) Structural basis for inhibition of the epidermal growth factor receptor by cetuximab. Cancer Cell 7: 301-311. (Pubitemid 40544648)
-
(2005)
Cancer Cell
, vol.7
, Issue.4
, pp. 301-311
-
-
Li, S.1
Schmitz, K.R.2
Jeffrey, P.D.3
Wiltzius, J.J.W.4
Kussie, P.5
Ferguson, K.M.6
-
28
-
-
33644839662
-
Structural model of the mAb 806-EGFR complex using computational docking followed by computational and experimental mutagenesis
-
DOI 10.1016/j.str.2005.11.022, PII S0969212606000736
-
Sivasubramanian A, Chao G, Pressler HM, Wittrup KD, Gray JJ (2006) Structural model of the mAb 806-EGFR complex using computational docking followed by computational and experimental mutagenesis. Structure 14: 401-414. (Pubitemid 43363474)
-
(2006)
Structure
, vol.14
, Issue.3
, pp. 401-414
-
-
Sivasubramanian, A.1
Chao, G.2
Pressler, H.M.3
Wittrup, K.D.4
Gray, J.J.5
-
29
-
-
65249179550
-
Antibodies specifically targeting a locally misfolded region of tumor associated EGFR
-
Garrett TP, Burgess AW, Gan HK, Luwor RB, Cartwright G, et al. (2009) Antibodies specifically targeting a locally misfolded region of tumor associated EGFR. Proc Natl Acad Sci U S A 106: 5082-5087.
-
(2009)
Proc Natl Acad Sci U S A
, vol.106
, pp. 5082-5087
-
-
Garrett, T.P.1
Burgess, A.W.2
Gan, H.K.3
Luwor, R.B.4
Cartwright, G.5
-
30
-
-
34247251270
-
A phase I clinical trial with monoclonal antibody ch806 targeting transitional state and mutant epidermal growth factor receptors
-
DOI 10.1073/pnas.0611693104
-
Scott AM, Lee FT, Tebbutt N, Herbertson R, Gill SS, et al. (2007) A phase I clinical trial with monoclonal antibody ch806 targeting transitional state and mutant epidermal growth factor receptors. Proc Natl Acad Sci U S A 104: 4071-4076. (Pubitemid 47181580)
-
(2007)
Proceedings of the National Academy of Sciences of the United States of America
, vol.104
, Issue.10
, pp. 4071-4076
-
-
Scott, A.M.1
Lee, F.-T.2
Tebbutt, N.3
Herbertson, R.4
Gill, S.S.5
Liu, Z.6
Skrinos, E.7
Murone, C.8
Saunder, T.H.9
Chappell, B.10
Papenfuss, A.T.11
Poon, A.M.T.12
Hopkins, W.13
Smyth, F.E.14
MacGregor, D.15
Cher, L.M.16
Jungbluth, A.A.17
Brechbiel, M.W.18
Murphy, R.19
Burgess, A.W.20
Hoffman, E.W.21
Johns, T.G.22
Old, L.J.23
more..
-
32
-
-
0038237369
-
Taking geometry to its edge: Fast unbound rigid (and hinge-bent) docking
-
DOI 10.1002/prot.10397
-
Schneidman-Duhovny D, Inbar Y, Polak V, Shatsky M, Halperin I, et al. (2003) Taking geometry to its edge: fast unbound rigid (and hinge-bent) docking. Proteins 52: 107-112. (Pubitemid 36648858)
-
(2003)
Proteins: Structure, Function and Genetics
, vol.52
, Issue.1
, pp. 107-112
-
-
Schneidman-Duhovny, D.1
Inbar, Y.2
Polak, V.3
Shatsky, M.4
Halperin, I.5
Benyamini, H.6
Barzilai, A.7
Dror, O.8
Haspel, N.9
Nussinov, R.10
Wolfson, H.J.11
-
33
-
-
0038820062
-
Features of a Smad3 MH1-DNA complex: Roles of water and zinc in DNA binding
-
DOI 10.1074/jbc.C300134200
-
Chai J, Wu JW, Yan N, Massague J, Pavletich NP, et al. (2003) Features of a Smad3 MH1-DNA complex. Roles of water and zinc in DNA binding. J Biol Chem 278: 20327-20331. (Pubitemid 36799232)
-
(2003)
Journal of Biological Chemistry
, vol.278
, Issue.22
, pp. 20327-20331
-
-
Chai, J.1
Wu, J.-W.2
Yan, N.3
Massague, J.4
Pavletich, N.P.5
Shi, Y.6
-
34
-
-
2442506874
-
Paramagnetism-Based Refinement Strategy for the Solution Structure of Human alpha-Parvalbumin
-
DOI 10.1021/bi035879k
-
Baig I, Bertini I, Del Bianco C, Gupta YK, Lee YM, et al. (2004) Paramagnetism-based refinement strategy for the solution structure of human alpha-parvalbumin. Biochemistry 43: 5562-5573. (Pubitemid 38620948)
-
(2004)
Biochemistry
, vol.43
, Issue.18
, pp. 5562-5573
-
-
Baig, I.1
Bertini, I.2
Del, B.C.3
Gupta, Y.K.4
Lee, Y.-M.5
Luchinat, C.6
Quattrone, A.7
-
35
-
-
14144256681
-
Energy functions for protein design: Adjustment with protein-protein complex affinities, models for the unfolded state, and negative design of solubility and specificity
-
DOI 10.1016/j.jmb.2004.12.019
-
Pokala N, Handel TM (2005) Energy functions for protein design: adjustment with protein-protein complex affinities, models for the unfolded state, and negative design of solubility and specificity. J Mol Biol 347: 203-227. (Pubitemid 40283639)
-
(2005)
Journal of Molecular Biology
, vol.347
, Issue.1
, pp. 203-227
-
-
Pokala, N.1
Handel, T.M.2
-
36
-
-
0023447105
-
Three-dimensional structure of an antibody-antigen complex
-
Sheriff S, Silverton EW, Padlan EA, Cohen GH, Smith-Gill SJ, et al. (1987) Three-dimensional structure of an antibody-antigen complex. Proc Natl Acad Sci U S A 84: 8075-8079.
-
(1987)
Proc Natl Acad Sci U S A
, vol.84
, pp. 8075-8079
-
-
Sheriff, S.1
Silverton, E.W.2
Padlan, E.A.3
Cohen, G.H.4
Smith-Gill, S.J.5
-
37
-
-
22844444097
-
Water molecules in the antibody-antigen interface of the structure of the Fab HyHEL-5-lysozyme complex at 1.7 A resolution: Comparison with results from isothermal titration calorimetry
-
DOI 10.1107/S0907444905007870
-
Cohen GH, Silverton EW, Padlan EA, Dyda F, Wibbenmeyer JA, et al. (2005) Water molecules in the antibody-antigen interface of the structure of the Fab HyHEL-5-lysozyme complex at 1.7 A resolution: comparison with results from isothermal titration calorimetry. Acta Crystallogr D Biol Crystallogr 61: 628-633. (Pubitemid 44336735)
-
(2005)
Acta Crystallographica Section D: Biological Crystallography
, vol.61
, Issue.5
, pp. 628-633
-
-
Cohen, G.H.1
Silverton, E.W.2
Padlan, E.A.3
Dyda, F.4
Wibbenmeyer, J.A.5
Willson, R.C.6
Davies, D.R.7
-
38
-
-
35648995435
-
Mapping the epitopes of antibodies
-
Ladner RC (2007) Mapping the epitopes of antibodies. Biotechnol Genet Eng Rev 24: 1-30.
-
(2007)
Biotechnol Genet Eng Rev
, vol.24
, pp. 1-30
-
-
Ladner, R.C.1
-
39
-
-
0033977962
-
SCOP: A structural classification of proteins database
-
Lo Conte L, Ailey B, Hubbard TJ, Brenner SE, Murzin AG, et al. (2000) SCOP: a structural classification of proteins database. Nucleic Acids Res 28: 257-259. (Pubitemid 30047773)
-
(2000)
Nucleic Acids Research
, vol.28
, Issue.1
, pp. 257-259
-
-
Lo, C.L.1
Ailey, B.2
Hubbard, T.J.P.3
Brenner, S.E.4
Murzin, A.G.5
Chothia, C.6
-
40
-
-
13444280419
-
PDB-TM: Selection and membrane localization of transmembrane proteins in the protein data bank
-
DOI 10.1093/nar/gki002
-
Tusnady GE, Dosztanyi Z, Simon I (2005) PDB-TM: selection and membrane localization of transmembrane proteins in the protein data bank. Nucleic Acids Res 33: D275-278. (Pubitemid 40207877)
-
(2005)
Nucleic Acids Research
, vol.33
, Issue.DATABASE ISS.
-
-
Tusnady, G.E.1
Dosztanyi, Z.2
Simon, I.3
-
41
-
-
10244252813
-
Transmembrane proteins in the Protein Data Bank: Identification and classification
-
DOI 10.1093/bioinformatics/bth340
-
Tusnady GE, Dosztanyi Z, Simon I (2004) Transmembrane proteins in the Protein Data Bank: identification and classification. Bioinformatics 20: 2964-2972. (Pubitemid 39619188)
-
(2004)
Bioinformatics
, vol.20
, Issue.17
, pp. 2964-2972
-
-
Tusnady, G.E.1
Dosztanyi, Z.2
Simon, I.3
-
42
-
-
0032214622
-
Protein Data Bank (PDB): Database of three-dimensional structural information of biological macromolecules
-
DOI 10.1107/S0907444998009378
-
Sussman JL, Lin D, Jiang J, Manning NO, Prilusky J, et al. (1998) Protein Data Bank (PDB): database of three-dimensional structural information of biological macromolecules. Acta Crystallogr D Biol Crystallogr 54: 1078-1084. (Pubitemid 29000162)
-
(1998)
Acta Crystallographica Section D: Biological Crystallography
, vol.54
, Issue.6 I
, pp. 1078-1084
-
-
Sussman, J.L.1
Lin, D.2
Jiang, J.3
Manning, N.O.4
Prilusky, J.5
Ritter, O.6
Abola, E.E.7
-
43
-
-
79955917527
-
Human protein reference database and human proteinpedia as discovery resources for molecular biotechnology
-
Goel R, Muthusamy B, Pandey A, Prasad TS (2011) Human protein reference database and human proteinpedia as discovery resources for molecular biotechnology. Mol Biotechnol 48: 87-95.
-
(2011)
Mol Biotechnol
, vol.48
, pp. 87-95
-
-
Goel, R.1
Muthusamy, B.2
Pandey, A.3
Prasad, T.S.4
-
45
-
-
70349330141
-
Evolutionary conservation in multiple faces of protein interaction
-
Choi YS, Yang JS, Choi Y, Ryu SH, Kim S (2009) Evolutionary conservation in multiple faces of protein interaction. Proteins 77: 14-25.
-
(2009)
Proteins
, vol.77
, pp. 14-25
-
-
Choi, Y.S.1
Yang, J.S.2
Choi, Y.3
Ryu, S.H.4
Kim, S.5
-
46
-
-
77954292440
-
ConPlex: A server for the evolutionary conservation analysis of protein complex structures
-
Choi YS, Han SK, Kim J, Yang JS, Jeon J, et al. (2010) ConPlex: a server for the evolutionary conservation analysis of protein complex structures. Nucleic Acids Res 38: W450-456.
-
(2010)
Nucleic Acids Res
, vol.38
-
-
Choi, Y.S.1
Han, S.K.2
Kim, J.3
Yang, J.S.4
Jeon, J.5
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