SCOPUS 정보 검색 플랫폼

Journal of Computational Chemistry

Volumn 34, Issue 10, 2013, Pages 879-891

Structure-based redesign of proteins for minimal T-cell epitope content

(3) Choi, Yoonjoo a Griswold, Karl E b Bailey Kellogg, Chris a

a Dartmouth Department of Computer Science_Dartmouth College (United States)

b DARTMOUTH COLLEGE (United States)

Author keywords

biologics; flexible backbone protein design; Rosetta design; T cell epitope; therapeutic protein deimmunization

Indexed keywords

BIOLOGICS; PROTEIN DESIGN; ROSETTA; T-CELL EPITOPES; THERAPEUTIC PROTEIN;

DESIGN; EPITOPES; IMMUNE SYSTEM; T-CELLS;

PROTEINS;

EPITOPE; PROTEIN;

ARTICLE; BIOLOGY; CHEMICAL PHENOMENA; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER PROGRAM; IMMUNOLOGY; PROTEIN CONFORMATION;

COMPUTATIONAL BIOLOGY; EPITOPES, T-LYMPHOCYTE; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEINS; SOFTWARE;

EID: 84875227578 PISSN: 01928651 EISSN: 1096987X Source Type: Journal
DOI: 10.1002/jcc.23213 Document Type: Article

Times cited : (18)

References (60)

1
- 84864317387
- Nat. Med. 2012, 18, 636.
- (2012) Nat. Med. , vol.18 , pp. 636

2
- 83255165688
- S. Aggarwal, Nat. Biotechnol. 2011, 29, 1083.
- (2011) Nat. Biotechnol. , vol.29 , pp. 1083
- Aggarwal, S.¹

3
- 0022558297
- P. Jones, P. Dear, J. Foote, M. Neuberger, G. Winter, Nature, 1986, 321, 522.
- (1986) Nature , vol.321 , pp. 522
- Jones, P.¹ Dear, P.² Foote, J.³ Neuberger, M.⁴ Winter, G.⁵

4
- 17644378667
- W. Hwang, J. Foote, Methods. 2005, 36, 3.
- (2005) Methods. , vol.36 , pp. 3
- Hwang, W.¹ Foote, J.²

5
- 35148851643
- A. Jakobovits, R. Amado, X. Yang, L. Roskos, G. Schwab, Nat. Biotechnol. 2007, 25, 1134.
- (2007) Nat. Biotechnol. , vol.25 , pp. 1134
- Jakobovits, A.¹ Amado, R.² Yang, X.³ Roskos, L.⁴ Schwab, G.⁵

6
- 79952399087
- A. Bradbury, S. Sidhu, S. Dübel, J. McCafferty, Nat. Biotechnol., 2011, 29, 245.
- (2011) Nat. Biotechnol. , vol.29 , pp. 245
- Bradbury, A.¹ Sidhu, S.² Dübel, S.³ McCafferty, J.⁴

7
- 84858631195
- S. Kontos, J. Hubbell, Chem. Soc. Rev. 2012, 41, 2686.
- (2012) Chem. Soc. Rev. , vol.41 , pp. 2686
- Kontos, S.¹ Hubbell, J.²

8
- 0036598634
- H. Schellekens, Nat. Rev. Drug Discov. 2002, 1, 457.
- (2002) Nat. Rev. Drug Discov. , vol.1 , pp. 457
- Schellekens, H.¹

9
- 33644634447
- A. De Groot, P. Knopp, W. Martin, Dev. Biol. (Basel). 2005, 122, 171.
- (2005) Dev. Biol. (Basel). , vol.122 , pp. 171
- De Groot, A.¹ Knopp, P.² Martin, W.³

10
- 63749128279
- A. De Groot, W. Martin, Clin. Immunol. 2009, 131, 189.
- (2009) Clin. Immunol. , vol.131 , pp. 189
- De Groot, A.¹ Martin, W.²

11
- 84903665310
- A. De Groot, T. Cohen, L. Moise, W. Martin, ESACT Proc. 2012, 5, 525.
- (2012) ESACT Proc. , vol.5 , pp. 525
- De Groot, A.¹ Cohen, T.² Moise, L.³ Martin, W.⁴

12
- 0036218529
- P. Warmerdam, S. Plaisance, K. Vanderlick, P. Vandervoort, K. Brepoels, D. Collen, M. De Maeyer, J. Thromb. Haemost. 2002, 87, 666.
- (2002) J. Thromb. Haemost. , vol.87 , pp. 666
- Warmerdam, P.¹ Plaisance, S.² Vanderlick, K.³ Vandervoort, P.⁴ Brepoels, K.⁵ Collen, D.⁶ De Maeyer, M.⁷

13
- 28044433859
- F. Harding, A. Liu, M. Stickler, O. Razo, R. Chin, N. Faravashi, W. Viola, T. Graycar, V. Yeung, W. Aehle, D. Meijer, S. Wong, M. Rashid, A. Valdes, V. Schellenberger, Mol. Cancer Ther. 2005, 4, 1791.
- (2005) Mol. Cancer Ther. , vol.4 , pp. 1791
- Harding, F.¹ Liu, A.² Stickler, M.³ Razo, O.⁴ Chin, R.⁵ Faravashi, N.⁶ Viola, W.⁷ Graycar, T.⁸ Yeung, V.⁹ Aehle, W.¹⁰ Meijer, D.¹¹ Wong, S.¹² Rashid, M.¹³ Valdes, A.¹⁴ Schellenberger, V.¹⁵

14
- 20144384746
- S. Tangri, B. Mothe, J. Eisenbraun, J. Sidney, S. Southwood, K. Briggs, J. Zinckgraf, P. Bilsel, M. Newman, R. Chesnut, C. LiCalsi, A. Sette, J. Immunol. 2005, 174, 3187.
- (2005) J. Immunol. , vol.174 , pp. 3187
- Tangri, S.¹ Mothe, B.² Eisenbraun, J.³ Sidney, J.⁴ Southwood, S.⁵ Briggs, K.⁶ Zinckgraf, J.⁷ Bilsel, P.⁸ Newman, M.⁹ Chesnut, R.¹⁰ Licalsi, C.¹¹ Sette, A.¹²

15
- 84857355243
- L. Moise, C. Song, W. Martin, R. Tassone, A. De Groot, D. Scott, Clin Immunol. 2012, 142, 320.
- (2012) Clin Immunol. , vol.142 , pp. 320
- Moise, L.¹ Song, C.² Martin, W.³ Tassone, R.⁴ De Groot, A.⁵ Scott, D.⁶

16
- 66149112273
- W. DeLano, The PyMOL molecular graphics system (ver. 1.4.1).
- The PyMOL Molecular Graphics System (Ver. 1.4.1)
- Delano, W.¹

17
- 34250635170
- J. Tong, T. Tan, S. Ranganathan, Brief. Bioinform. 2007, 8, 96.
- (2007) Brief. Bioinform. , vol.8 , pp. 96
- Tong, J.¹ Tan, T.² Ranganathan, S.³

18
- 42949139524
- P. Wang, J. Sidney, C. Dow, B. Mothe, A. Sette, B. Peters, PLoS Comp. Biol. 2008, 4, e1000048.
- (2008) PLoS Comp. Biol. , vol.4
- Wang, P.¹ Sidney, J.² Dow, C.³ Mothe, B.⁴ Sette, A.⁵ Peters, B.⁶

19
- 83155180577
- L. Zhang, K. Udaka, H. Mamitsuka, S. Zhu, Brief. Bioinform. 2012, 13, 350.
- (2012) Brief. Bioinform. , vol.13 , pp. 350
- Zhang, L.¹ Udaka, K.² Mamitsuka, H.³ Zhu, S.⁴

20
- 84903685937
- J. Cantor, T. Yoo, A. Dixit, B. Iverson, T. Forsthuber, G. Georgiou, PNAS. 2011, 108, 1271.
- (2011) PNAS. , vol.108 , pp. 1271
- Cantor, J.¹ Yoo, T.² Dixit, A.³ Iverson, B.⁴ Forsthuber, T.⁵ Georgiou, G.⁶

21
- 84867004820
- doi:10.1093/protein/gzs044
- D. Osipovitch, A. Parker, C. Makokha, J. Desrosiers, W. Kett, L. Moise, C. Bailey-Kellogg, K. Griswold, Protein. Eng. Des. Sel. 2012; doi:10.1093/protein/gzs044.
- (2012) Protein. Eng. Des. Sel.
- Osipovitch, D.¹ Parker, A.² Makokha, C.³ Desrosiers, J.⁴ Kett, W.⁵ Moise, L.⁶ Bailey-Kellogg, C.⁷ Griswold, K.⁸

22
- 33846111016
- W. Fischer, S. Perkins, J. Theiler, T. Bhattacharya, K. Yusim, R. Funkhouser, C. Kuiken, B. Haynes, N. Letvin, B. Walker, B. Hahn, B. Korber, Nat. Med. 2006, 13, 100.
- (2006) Nat. Med. , vol.13 , pp. 100
- Fischer, W.¹ Perkins, S.² Theiler, J.³ Bhattacharya, T.⁴ Yusim, K.⁵ Funkhouser, R.⁶ Kuiken, C.⁷ Haynes, B.⁸ Letvin, N.⁹ Walker, B.¹⁰ Hahn, B.¹¹ Korber, B.¹²

23
- 70350072668
- L. Moise, J. McMurry, S. Buus, S. Frey, W. Martin, A. De Groot, Vaccine 2009, 27, 6471.
- (2009) Vaccine , vol.27 , pp. 6471
- Moise, L.¹ McMurry, J.² Buus, S.³ Frey, S.⁴ Martin, W.⁵ De Groot, A.⁶

24
- 84864032169
- A. De Groot, L. Levitz, M. Ardito, G. Skowron, K. Mayer, S. Buus, C. Boyle, W. Martin, Hum. Vaccin. Immunother. 2012, 8, 987.
- (2012) Hum. Vaccin. Immunother. , vol.8 , pp. 987
- De Groot, A.¹ Levitz, L.² Ardito, M.³ Skowron, G.⁴ Mayer, K.⁵ Buus, S.⁶ Boyle, C.⁷ Martin, W.⁸

25
- 77950673538
- A. Parker, W. Zheng, K. Griswold, C. Bailey-Kellogg, BMC Bioinf. 2010, 11, 180.
- (2010) BMC Bioinf. , vol.11 , pp. 180
- Parker, A.¹ Zheng, W.² Griswold, K.³ Bailey-Kellogg, C.⁴

26
- 80052071931
- A. Parker, K. Griswold, C. Bailey-Kellogg, J. Bioinf. Comput. Biol. 2011, 9, 207.
- (2011) J. Bioinf. Comput. Biol. , vol.9 , pp. 207
- Parker, A.¹ Griswold, K.² Bailey-Kellogg, C.³

27
- 84860790543
- A. Parker, K. Griswold, C. Bailey-Kellogg, Res. Comput. Mol. Biol. 2012, 7262, 184.
- (2012) Res. Comput. Mol. Biol. , vol.7262 , pp. 184
- Parker, A.¹ Griswold, K.² Bailey-Kellogg, C.³

28
- 84856786576
- L. He, A. Friedman, C. Bailey-Kellogg, Proteins, 2012, 80, 790.
- (2012) Proteins , vol.80 , pp. 790
- He, L.¹ Friedman, A.² Bailey-Kellogg, C.³

29
- 80052334922
- P. Huang, Y.A. Ban, F. Richter, I. Andre, R. Vernon, W.R. Schief, D. Baker, PLoS One 2011, 6, e24109.
- (2011) PLoS One , vol.6
- Huang, P.¹ Ban, Y.A.² Richter, F.³ Andre, I.⁴ Vernon, R.⁵ Schief, W.R.⁶ Baker, D.⁷

30
- 0345306764
- B. Kuhlman, G. Dantas, G. Ireton, G. Varani, B. Stoddard, D. Baker, Science 2003, 302, 1364.
- (2003) Science , vol.302 , pp. 1364
- Kuhlman, B.¹ Dantas, G.² Ireton, G.³ Varani, G.⁴ Stoddard, B.⁵ Baker, D.⁶

31
- 78650414310
- B. Correia, Y. Ban, D. Friend, K. Ellingson, H. Xu, E. Boni, T. Bradley-Hewitt, J. Bruhn-Johannsen, L. Stamatatos, R. Strong, W. Schief, J. Mol. Biol. 2011, 405, 284.
- (2011) J. Mol. Biol. , vol.405 , pp. 284
- Correia, B.¹ Ban, Y.² Friend, D.³ Ellingson, K.⁴ Xu, H.⁵ Boni, E.⁶ Bradley-Hewitt, T.⁷ Bruhn-Johannsen, J.⁸ Stamatatos, L.⁹ Strong, R.¹⁰ Schief, W.¹¹

32
- 79953058640
- D. Sammond, D. Bosch, G. Butterfoss, C. Purbeck, M. Machius, D. Siderovski, B. Kuhlman, J. Am. Chem. Soc. 2011, 133, 4190.
- (2011) J. Am. Chem. Soc. , vol.133 , pp. 4190
- Sammond, D.¹ Bosch, D.² Butterfoss, G.³ Purbeck, C.⁴ MacHius, M.⁵ Siderovski, D.⁶ Kuhlman, B.⁷

33
- 0036137241
- H. Singh, G. Raghava, Bioinformatics, 2001, 17, 1236.
- (2001) Bioinformatics , vol.17 , pp. 1236
- Singh, H.¹ Raghava, G.²

34
- 79956017135
- S. Fleishman, T. Whitehead, D. Ekiert, C. Dreyfus, J. Corn, E. Strauch, I. Wilson, D. Baker, Science, 2011, 332, 816.
- (2011) Science , vol.332 , pp. 816
- Fleishman, S.¹ Whitehead, T.² Ekiert, D.³ Dreyfus, C.⁴ Corn, J.⁵ Strauch, E.⁶ Wilson, I.⁷ Baker, D.⁸

35
- 0034641749
- B. Kuhlman, D. Baker, PNAS 2000, 97, 10383.
- (2000) PNAS , vol.97 , pp. 10383
- Kuhlman, B.¹ Baker, D.²

36
- 78650905964
- A. Leaver-Fay, M. Tyka, S. Lewis, O. Lange, J. Thompson, R. Jacak, K. Kaufman, P. Renfrew, C. Smith, W. Sheffler, I. Davis, S. Cooper, A. Treuille, D. Mandell, F. Richter, Y. Ban, S. Fleishman, J. Corn, D. Kim, S. Lyskov, M. Berrondo, S. Mentzer, Z. Popovic, J. Havranek, J. Karanicolas, R. Das, J. Meiler, T. Kortemme, J. Gray, B. Kuhlman, D. Baker, P. Bradley, Methods. Enzymol. 2011, 487, 545.
- (2011) Methods. Enzymol. , vol.487 , pp. 545
- Leaver-Fay, A.¹ Tyka, M.² Lewis, S.³ Lange, O.⁴ Thompson, J.⁵ Jacak, R.⁶ Kaufman, K.⁷ Renfrew, P.⁸ Smith, C.⁹ Sheffler, W.¹⁰ Davis, I.¹¹ Cooper, S.¹² Treuille, A.¹³ Mandell, D.¹⁴ Richter, F.¹⁵ Ban, Y.¹⁶ Fleishman, S.¹⁷ Corn, J.¹⁸ Kim, D.¹⁹ Lyskov, S.²⁰ more..

37
- 33745033790
- G. Butterfoss, B. Kuhlman, Annu. Rev. Biophys. Biomol. Struct. 2006, 35, 49.
- (2006) Annu. Rev. Biophys. Biomol. Struct. , vol.35 , pp. 49
- Butterfoss, G.¹ Kuhlman, B.²

38
- 79959615159
- S. Fleishman, A. Leaver-Fay, J. Corn, E. Strauch, S. Khare, N. Koga, J. Ashworth, P. Murphy, F. Richter, G. Lemmon, J. Meiler, D. Baker, PLoS One 2011, 6, e20161.
- (2011) PLoS One , vol.6
- Fleishman, S.¹ Leaver-Fay, A.² Corn, J.³ Strauch, E.⁴ Khare, S.⁵ Koga, N.⁶ Ashworth, J.⁷ Murphy, P.⁸ Richter, F.⁹ Lemmon, G.¹⁰ Meiler, J.¹¹ Baker, D.¹²

39
- 58149463441
- W. Sheffler, D. Baker, Protein. Sci. 2009, 18, 229.
- (2009) Protein. Sci. , vol.18 , pp. 229
- Sheffler, W.¹ Baker, D.²

40
- 0032055915
- S. Southwood, J. Sidney, A. Kondo, M. del Guercio, E. Appella, S. Hoffman, R. Kubo, R. Chesnut, H. Grey, A. Sette, J. Immunol. 1998, 160, 3363.
- (1998) J. Immunol. , vol.160 , pp. 3363
- Southwood, S.¹ Sidney, J.² Kondo, A.³ Del Guercio, M.⁴ Appella, E.⁵ Hoffman, S.⁶ Kubo, R.⁷ Chesnut, R.⁸ Grey, H.⁹ Sette, A.¹⁰

41
- 34548089690
- R. Dinglasan, D. Kalume, S. Kanzok, A. Ghosh, O. Muratova, A. Pandey, M. Jacobs-Lorena, PNAS, 2007, 104, 13461.
- (2007) PNAS , vol.104 , pp. 13461
- Dinglasan, R.¹ Kalume, D.² Kanzok, S.³ Ghosh, A.⁴ Muratova, O.⁵ Pandey, A.⁶ Jacobs-Lorena, M.⁷

42
- 34250831523
- E. Klyushnenkova, D. Kouiavskaia, J. Kodak, A. Vandenbark, R. Alexander, Prostate 2007, 67, 1019.
- (2007) Prostate , vol.67 , pp. 1019
- Klyushnenkova, E.¹ Kouiavskaia, D.² Kodak, J.³ Vandenbark, A.⁴ Alexander, R.⁵

43
- 32444438223
- A. Mustafa, F. Shaban, Tuberculosis 2006, 86, 115.
- (2006) Tuberculosis , vol.86 , pp. 115
- Mustafa, A.¹ Shaban, F.²

44
- 0030801002
- S. Altschul, T. Madden, A. Schaffer, J. Zhang, Z. Zhang, W. Miller, D. Lipman, Nucl. Acids Res. 1997, 25, 3389.
- (1997) Nucl. Acids Res. , vol.25 , pp. 3389
- Altschul, S.¹ Madden, T.² Schaffer, A.³ Zhang, J.⁴ Zhang, Z.⁵ Miller, W.⁶ Lipman, D.⁷

45
- 0036053169
- F. Indiveri, G. Murdaca, Rev. Clin. Exp. Hematol. 2002, 1, 7.
- (2002) Rev. Clin. Exp. Hematol. , vol.1 , pp. 7
- Indiveri, F.¹ Murdaca, G.²

46
- 0032188942
- R. Syed, S. Reid, C. Li, J. Cheetham, K. Aoki, B. Liu, H. Zhan, T. Osslund, A. Chirino, J. Zhang, J. Finer-Moore, S. Elliott, K. Sitney, B. Katz, D. Matthews, J. Wendoloski, J. Egrie, R. Stroud, Nature 1998, 395, 511.
- (1998) Nature , vol.395 , pp. 511
- Syed, R.¹ Reid, S.² Li, C.³ Cheetham, J.⁴ Aoki, K.⁵ Liu, B.⁶ Zhan, H.⁷ Osslund, T.⁸ Chirino, A.⁹ Zhang, J.¹⁰ Finer-Moore, J.¹¹ Elliott, S.¹² Sitney, K.¹³ Katz, B.¹⁴ Matthews, D.¹⁵ Wendoloski, J.¹⁶ Egrie, J.¹⁷ Stroud, R.¹⁸

47
- 0031596034
- M. Parry, C. Fernandez-Catalan, A. Bergner, R. Huber, K. Hopfner, B. Schlott, K. Guhrs, W. Bode, Nat. Struct. Biol. 1998, 5, 917.
- (1998) Nat. Struct. Biol. , vol.5 , pp. 917
- Parry, M.¹ Fernandez-Catalan, C.² Bergner, A.³ Huber, R.⁴ Hopfner, K.⁵ Schlott, B.⁶ Guhrs, K.⁷ Bode, W.⁸

48
- 0030888405
- A. Rabijns, H. De Bondt, C. De Ranter, Nat. Struct. Biol. 1997, 4, 357.
- (1997) Nat. Struct. Biol. , vol.4 , pp. 357
- Rabijns, A.¹ De Bondt, H.² De Ranter, C.³

49
- 23144438711
- G. Wang, R.J. Dunbrack, Nucl. Acids. Res. 2005, 33, W94.
- (2005) Nucl. Acids. Res. , vol.33
- Wang, G.¹ Dunbrack, R.J.²

50
- 13444280419
- G. Tusnady, Z. Dosztanyi, I. Simon, Nucl. Acids. Res. 2005, 33, D275.
- (2005) Nucl. Acids. Res. , vol.33
- Tusnady, G.¹ Dosztanyi, Z.² Simon, I.³

51
- 10344232638
- Y. Zhang, J. Skolnick, Proteins 2004, 57, 702.
- (2004) Proteins , vol.57 , pp. 702
- Zhang, Y.¹ Skolnick, J.²

52
- 38549153238
- A. Andreeva, D. Howorth, J. Chandonia, S. Brenner, T. Hubbard, C. Chothia, A. Murzin, Nucl. Acids. Res. 2008, 36, D419.
- (2008) Nucl. Acids. Res. , vol.36
- Andreeva, A.¹ Howorth, D.² Chandonia, J.³ Brenner, S.⁴ Hubbard, T.⁵ Chothia, C.⁶ Murzin, A.⁷

53
- 58149187899
- A. Cuff, I. Sillitoe, T. Lewis, O. Redfern, R. Garratt, J. Thornton, C. Orengo, Nucl. Acids. Res. 2009, 37, D310.
- (2009) Nucl. Acids. Res. , vol.37
- Cuff, A.¹ Sillitoe, I.² Lewis, T.³ Redfern, O.⁴ Garratt, R.⁵ Thornton, J.⁶ Orengo, C.⁷

54
- 77951961719
- J. Xu, Y. Zhang, Bioinformatics 2010, 26, 889.
- (2010) Bioinformatics , vol.26 , pp. 889
- Xu, J.¹ Zhang, Y.²

55
- 0020475449
- J. Kyte, R. Doolittle, J. Mol. Biol. 1982, 157, 105.
- (1982) J. Mol. Biol. , vol.157 , pp. 105
- Kyte, J.¹ Doolittle, R.²

56
- 0020997912
- W. Kabsch, C. Sander, Biopolymers 1983, 22, 2577.
- (1983) Biopolymers , vol.22 , pp. 2577
- Kabsch, W.¹ Sander, C.²

57
- 56649099192
- R. Ujwal, D. Cascio, J.P. Colletier, S. Faham, J. Zhang, L. Toro, P. Ping, J. Abramson, PNAS 2008, 105, 17742.
- (2008) PNAS , vol.105 , pp. 17742
- Ujwal, R.¹ Cascio, D.² Colletier, J.P.³ Faham, S.⁴ Zhang, J.⁵ Toro, L.⁶ Ping, P.⁷ Abramson, J.⁸

58
- 72049087000
- M. Guo, Y.E. Chong, R. Shapiro, K. Beebe, X. Yang, P. Schimmel, Nature 2009, 462, 808.
- (2009) Nature , vol.462 , pp. 808
- Guo, M.¹ Chong, Y.E.² Shapiro, R.³ Beebe, K.⁴ Yang, X.⁵ Schimmel, P.⁶

59
- 2142738304
- G. Crooks, G. Hon, J. Chandonia, S. Brenner, Genome Res. 2004, 14, 1188.
- (2004) Genome Res. , vol.14 , pp. 1188
- Crooks, G.¹ Hon, G.² Chandonia, J.³ Brenner, S.⁴

60
- 84862025262
- T. Whitehead, A. Chevalier, Y. Song, C. Dreyfus, S. Fleishman, C. De Mattos, C. Myers, H. Kamisetty, P. Blair, I. Wilson, D. Baker, Nat. Biotechnol. 2012, 30, 543.
- (2012) Nat. Biotechnol. , vol.30 , pp. 543
- Whitehead, T.¹ Chevalier, A.² Song, Y.³ Dreyfus, C.⁴ Fleishman, S.⁵ De Mattos, C.⁶ Myers, C.⁷ Kamisetty, H.⁸ Blair, P.⁹ Wilson, I.¹⁰ Baker, D.¹¹

* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.