-
1
-
-
11844301261
-
Recent developments in the PHENIX software for automated crystallographic structure determination
-
Adams, P. D., K. Gopal, R. W. Grosse-Kunstleve, L. W. Hung, T. R. Ioerger, A. J. McCoy, N. W. Moriarty, R. K. Pai, R. J. Read, T. D. Romo, J. C. Sacchettini, N. K. Sauter, L. C. Storoni, and T. C. Terwilliger. 2004. Recent developments in the PHENIX software for automated crystallographic structure determination. J. Synchrotron Radiat. 11:53-55.
-
(2004)
J. Synchrotron Radiat.
, vol.11
, pp. 53-55
-
-
Adams, P.D.1
Gopal, K.2
Grosse-Kunstleve, R.W.3
Hung, L.W.4
Ioerger, T.R.5
McCoy, A.J.6
Moriarty, N.W.7
Pai, R.K.8
Read, R.J.9
Romo, T.D.10
Sacchettini, J.C.11
Sauter, N.K.12
Storoni, L.C.13
Terwilliger, T.C.14
-
2
-
-
73949133588
-
Role of HIV membrane in neutralization by two broadly neutralizing antibodies
-
Alam, S. M., M. Morelli, S. M. Dennison, H. X. Liao, R. Zhang, S. M. Xia, S. Rits-Volloch, L. Sun, S. C. Harrison, B. F. Haynes, and B. Chen. 2009. Role of HIV membrane in neutralization by two broadly neutralizing antibodies. Proc. Natl. Acad. Sci. U. S. A. 106:20234-20239.
-
(2009)
Proc. Natl. Acad. Sci. U. S. A.
, vol.106
, pp. 20234-20239
-
-
Alam, S.M.1
Morelli, M.2
Dennison, S.M.3
Liao, H.X.4
Zhang, R.5
Xia, S.M.6
Rits-Volloch, S.7
Sun, L.8
Harrison, S.C.9
Haynes, B.F.10
Chen, B.11
-
3
-
-
56449131391
-
Profiling the specificity of neutralizing antibodies in a large panel of plasmas from patients chronically infected with human immunodeficiency virus type 1 subtypes B and C
-
Binley, J. M., E. A. Lybarger, E. T. Crooks, M. S. Seaman, E. Gray, K. L. Davis, J. M. Decker, D. Wycuff, L. Harris, N. Hawkins, B. Wood, C. Nathe, D. Richman, G. D. Tomaras, F. Bibollet-Ruche, J. E. Robinson, L. Morris, G. M. Shaw, D. C. Montefiori, and J. R. Mascola. 2008. Profiling the specificity of neutralizing antibodies in a large panel of plasmas from patients chronically infected with human immunodeficiency virus type 1 subtypes B and C. J. Virol. 82:11651-11668.
-
(2008)
J. Virol.
, vol.82
, pp. 11651-11668
-
-
Binley, J.M.1
Lybarger, E.A.2
Crooks, E.T.3
Seaman, M.S.4
Gray, E.5
Davis, K.L.6
Decker, J.M.7
Wycuff, D.8
Harris, L.9
Hawkins, N.10
Wood, B.11
Nathe, C.12
Richman, D.13
Tomaras, G.D.14
Bibollet-Ruche, F.15
Robinson, J.E.16
Morris, L.17
Shaw, G.M.18
Montefiori, D.C.19
Mascola, J.R.20
more..
-
4
-
-
0026597444
-
Free R value: A novel statistical quantity for assessing the accuracy of crystal structures
-
Brunger, A. T. 1992. Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature 355:472-475.
-
(1992)
Nature
, vol.355
, pp. 472-475
-
-
Brunger, A.T.1
-
5
-
-
0028155283
-
Generation of human monoclonal antibodies against HIV-1 proteins; electrofusion and Epstein-Barr virus transformation for peripheral blood lymphocyte immortalization
-
Buchacher, A., R. Predl, K. Strutzenberger, W. Steinfellner, A. Trkola, M. Purtscher, G. Gruber, C. Tauer, F. Steindl, A. Jungbauer, et al. 1994. Generation of human monoclonal antibodies against HIV-1 proteins; electrofusion and Epstein-Barr virus transformation for peripheral blood lymphocyte immortalization. AIDS Res. Hum. Retroviruses 10:359-369.
-
(1994)
AIDS Res. Hum. Retroviruses
, vol.10
, pp. 359-369
-
-
Buchacher, A.1
Predl, R.2
Strutzenberger, K.3
Steinfellner, W.4
Trkola, A.5
Purtscher, M.6
Gruber, G.7
Tauer, C.8
Steindl, F.9
Jungbauer, A.10
-
6
-
-
0036719574
-
Antibodies, viruses and vaccines
-
Burton, D. R. 2002. Antibodies, viruses and vaccines. Nat. Rev. Immunol. 2:706-713.
-
(2002)
Nat. Rev. Immunol.
, vol.2
, pp. 706-713
-
-
Burton, D.R.1
-
7
-
-
0027985431
-
Efficient neutralization of primary isolates of HIV-1 by a recombinant human monoclonal antibody
-
Burton, D. R., J. Pyati, R. Koduri, S. J. Sharp, G. B. Thornton, P. W. Parren, L. S. Sawyer, R. M. Hendry, N. Dunlop, P. L. Nara, et al. 1994. Efficient neutralization of primary isolates of HIV-1 by a recombinant human monoclonal antibody. Science 266:1024-1027.
-
(1994)
Science
, vol.266
, pp. 1024-1027
-
-
Burton, D.R.1
Pyati, J.2
Koduri, R.3
Sharp, S.J.4
Thornton, G.B.5
Parren, P.W.6
Sawyer, L.S.7
Hendry, R.M.8
Dunlop, N.9
Nara, P.L.10
-
9
-
-
70450182950
-
Structural basis of immune evasion at the site of CD4 attachment on HIV-1 gp120
-
Chen, L., Y. D. Kwon, T. Zhou, X. Wu, S. O'Dell, L. Cavacini, A. J. Hessell, M. Pancera, M. Tang, L. Xu, Z. Y. Yang, M. Y. Zhang, J. Arthos, D. R. Burton, D. S. Dimitrov, G. J. Nabel, M. R. Posner, J. Sodroski, R. Wyatt, J. R. Mascola, and P. D. Kwong. 2009. Structural basis of immune evasion at the site of CD4 attachment on HIV-1 gp120. Science 326:1123-1127.
-
(2009)
Science
, vol.326
, pp. 1123-1127
-
-
Chen, L.1
Kwon, Y.D.2
Zhou, T.3
Wu, X.4
O'Dell, S.5
Cavacini, L.6
Hessell, A.J.7
Pancera, M.8
Tang, M.9
Xu, L.10
Yang, Z.Y.11
Zhang, M.Y.12
Arthos, J.13
Burton, D.R.14
Dimitrov, D.S.15
Nabel, G.J.16
Posner, M.R.17
Sodroski, J.18
Wyatt, R.19
Mascola, J.R.20
Kwong, P.D.21
more..
-
10
-
-
74549178560
-
MolProbity: All-atom structure validation for macromolecular crystallography
-
Chen, V. B., W. B. Arendall III, J. J. Headd, D. A. Keedy, R. M. Immormino, G. J. Kapral, L. W. Murray, J. S. Richardson, and D. C. Richardson. 2010. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr. D Biol. Crystallogr. 66:12-21.
-
(2010)
Acta Crystallogr. D Biol. Crystallogr.
, vol.66
, pp. 12-21
-
-
Chen, V.B.1
Arendall III, W.B.2
Headd, J.J.3
Keedy, D.A.4
Immormino, R.M.5
Kapral, G.J.6
Murray, L.W.7
Richardson, J.S.8
Richardson, D.C.9
-
11
-
-
0028103275
-
The CCP4 suite: Programs for protein crystallography
-
Collaborative Computational Project No. 4
-
Collaborative Computational Project No. 4 1994. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D Biol. Crystallogr. 50:760-763.
-
(1994)
Acta Crystallogr. D Biol. Crystallogr.
, vol.50
, pp. 760-763
-
-
-
12
-
-
0037227422
-
Analysis of the antigen combining site: Correlations between length and sequence composition of the hypervariable loops and the nature of the antigen
-
Collis, A. V., A. P. Brouwer, and A. C. Martin. 2003. Analysis of the antigen combining site: correlations between length and sequence composition of the hypervariable loops and the nature of the antigen. J. Mol. Biol. 325:337-354.
-
(2003)
J. Mol. Biol.
, vol.325
, pp. 337-354
-
-
Collis, A.V.1
Brouwer, A.P.2
Martin, A.C.3
-
13
-
-
33746414364
-
Considerations for the refinement of low-resolution crystal structures
-
DeLaBarre, B., and A. T. Brunger. 2006. Considerations for the refinement of low-resolution crystal structures. Acta Crystallogr. D Biol. Crystallogr. 62:923-932.
-
(2006)
Acta Crystallogr. D Biol. Crystallogr.
, vol.62
, pp. 923-932
-
-
DeLaBarre, B.1
Brunger, A.T.2
-
15
-
-
77953673590
-
Therapeutic antibodies, vaccines and antibodyomes
-
Dimitrov, D. S. 2010. Therapeutic antibodies, vaccines and antibodyomes. mAbs 2:347-356.
-
(2010)
mAbs
, vol.2
, pp. 347-356
-
-
Dimitrov, D.S.1
-
16
-
-
73949084963
-
Breadth of human immunodeficiency virus-specific neutralizing activity in sera: Clustering analysis and association with clinical variables
-
Doria-Rose, N. A., R. M. Klein, M. G. Daniels, S. O'Dell, M. Nason, A. Lapedes, T. Bhattacharya, S. A. Migueles, R. T. Wyatt, B. T. Korber, J. R. Mascola, and M. Connors. 2010. Breadth of human immunodeficiency virus-specific neutralizing activity in sera: clustering analysis and association with clinical variables. J. Virol. 84:1631-1636.
-
(2010)
J. Virol.
, vol.84
, pp. 1631-1636
-
-
Doria-Rose, N.A.1
Klein, R.M.2
Daniels, M.G.3
O'Dell, S.4
Nason, M.5
Lapedes, A.6
Bhattacharya, T.7
Migueles, S.A.8
Wyatt, R.T.9
Korber, B.T.10
Mascola, J.R.11
Connors, M.12
-
17
-
-
32944477067
-
The rational design of an AIDS vaccine
-
Douek, D. C., P. D. Kwong, and G. J. Nabel. 2006. The rational design of an AIDS vaccine. Cell 124:677-681.
-
(2006)
Cell
, vol.124
, pp. 677-681
-
-
Douek, D.C.1
Kwong, P.D.2
Nabel, G.J.3
-
19
-
-
0028871926
-
Dali: A network tool for protein structure comparison
-
Holm, L., and C. Sander. 1995. Dali: a network tool for protein structure comparison. Trends Biochem. Sci. 20:478-480.
-
(1995)
Trends Biochem. Sci.
, vol.20
, pp. 478-480
-
-
Holm, L.1
Sander, C.2
-
20
-
-
1842639184
-
Crystal structure of the calcium-stabilized human factor IX Gla domain bound to a conformation-specific anti-factor IX antibody
-
Huang, M., B. C. Furie, and B. Furie. 2004. Crystal structure of the calcium-stabilized human factor IX Gla domain bound to a conformation-specific anti-factor IX antibody. J. Biol. Chem. 279:14338-14346.
-
(2004)
J. Biol. Chem.
, vol.279
, pp. 14338-14346
-
-
Huang, M.1
Furie, B.C.2
Furie, B.3
-
21
-
-
84889120137
-
Improved methods for building protein models in electron density maps and the location of errors in these models
-
Jones, T. A., J. Y. Zou, S. W. Cowan, and M. Kjeldgaard. 1991. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47(Pt. 2):110-119.
-
(1991)
Acta Crystallogr. A
, vol.47
, Issue.PART 2
, pp. 110-119
-
-
Jones, T.A.1
Zou, J.Y.2
Cowan, S.W.3
Kjeldgaard, M.4
-
22
-
-
77950803157
-
Ablation of the complementarity-determining region H3 apex of the anti-HIV-1 broadly neutralizing antibody 2F5 abrogates neutralizing capacity without affecting core epitope binding
-
Julien, J. P., N. Huarte, R. Maeso, S. G. Taneva, A. Cunningham, J. L. Nieva, and E. F. Pai. 2010. Ablation of the complementarity-determining region H3 apex of the anti-HIV-1 broadly neutralizing antibody 2F5 abrogates neutralizing capacity without affecting core epitope binding. J. Virol. 84:4136-4147.
-
(2010)
J. Virol.
, vol.84
, pp. 4136-4147
-
-
Julien, J.P.1
Huarte, N.2
Maeso, R.3
Taneva, S.G.4
Cunningham, A.5
Nieva, J.L.6
Pai, E.F.7
-
23
-
-
0004032583
-
-
5th ed. National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, MD
-
Kabat, E. A., T. T. Wu, H. M. Perry, K. S. Gottesman, and C. Foeller. 1991. Sequences of proteins of immunological interest, 5th ed. National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, MD.
-
(1991)
Sequences of Proteins of Immunological Interest
-
-
Kabat, E.A.1
Wu, T.T.2
Perry, H.M.3
Gottesman, K.S.4
Foeller, C.5
-
24
-
-
66149132686
-
Examination of the contributions of size and avidity to the neutralization mechanisms of the anti-HIV antibodies b12 and 4E10
-
Klein, J. S., P. N. Gnanapragasam, R. P. Galimidi, C. P. Foglesong, A. P. West, Jr., and P. J. Bjorkman. 2009. Examination of the contributions of size and avidity to the neutralization mechanisms of the anti-HIV antibodies b12 and 4E10. Proc. Natl. Acad. Sci. U. S. A. 106:7385-7390.
-
(2009)
Proc. Natl. Acad. Sci. U. S. A.
, vol.106
, pp. 7385-7390
-
-
Klein, J.S.1
Gnanapragasam, P.N.2
Galimidi, R.P.3
Foglesong, C.P.4
West Jr., A.P.5
Bjorkman, P.J.6
-
25
-
-
0035865051
-
Novel secondary Ig VH gene rearrangement and in-frame Ig heavy chain complementarity-determining region III insertion/deletion variants in de novo follicular lymphoma
-
Kobrin, C., M. Bendandi, and L. Kwak. 2001. Novel secondary Ig VH gene rearrangement and in-frame Ig heavy chain complementarity-determining region III insertion/deletion variants in de novo follicular lymphoma. J. Immunol. 166:2235-2243.
-
(2001)
J. Immunol.
, vol.166
, pp. 2235-2243
-
-
Kobrin, C.1
Bendandi, M.2
Kwak, L.3
-
26
-
-
0035162494
-
Evolutionary and immunological implications of contemporary HIV-1 variation
-
Korber, B., B. Gaschen, K. Yusim, R. Thakallapally, C. Kesmir, and V. Detours. 2001. Evolutionary and immunological implications of contemporary HIV-1 variation. Br. Med. Bull. 58:19-42.
-
(2001)
Br. Med. Bull.
, vol.58
, pp. 19-42
-
-
Korber, B.1
Gaschen, B.2
Yusim, K.3
Thakallapally, R.4
Kesmir, C.5
Detours, V.6
-
27
-
-
0033548254
-
Probability analysis of variational crystallization and its application to gp120, the exterior envelope glycoprotein of type 1 human immunodeficiency virus (HIV-1)
-
Kwong, P. D., R. Wyatt, E. Desjardins, J. Robinson, J. S. Culp, B. D. Hellmig, R. W. Sweet, J. Sodroski, and W. A. Hendrickson. 1999. Probability analysis of variational crystallization and its application to gp120, the exterior envelope glycoprotein of type 1 human immunodeficiency virus (HIV-1). J. Biol. Chem. 274:4115-4123.
-
(1999)
J. Biol. Chem.
, vol.274
, pp. 4115-4123
-
-
Kwong, P.D.1
Wyatt, R.2
Desjardins, E.3
Robinson, J.4
Culp, J.S.5
Hellmig, B.D.6
Sweet, R.W.7
Sodroski, J.8
Hendrickson, W.A.9
-
28
-
-
36448991500
-
Clustal W and Clustal X
-
version 2.0
-
Larkin, M. A., G. Blackshields, N. P. Brown, R. Chenna, P. A. McGettigan, H. McWilliam, F. Valentin, I. M. Wallace, A. Wilm, R. Lopez, J. D. Thompson, T. J. Gibson, and D. G. Higgins. 2007. Clustal W and Clustal X version 2.0. Bioinformatics 23:2947-2948.
-
(2007)
Bioinformatics
, vol.23
, pp. 2947-2948
-
-
Larkin, M.A.1
Blackshields, G.2
Brown, N.P.3
Chenna, R.4
McGettigan, P.A.5
McWilliam, H.6
Valentin, F.7
Wallace, I.M.8
Wilm, A.9
Lopez, R.10
Thompson, J.D.11
Gibson, T.J.12
Higgins, D.G.13
-
29
-
-
58149316094
-
IMGT, the international ImMuno- GeneTics information system
-
Lefranc, M. P., V. Giudicelli, C. Ginestoux, J. Jabado-Michaloud, G. Folch, F. Bellahcene, Y. Wu, E. Gemrot, X. Brochet, J. Lane, L. Regnier, F. Ehrenmann, G. Lefranc, and P. Duroux. 2009. IMGT, the international ImMuno- GeneTics information system. Nucleic Acids Res. 37:D1006-D1012.
-
(2009)
Nucleic Acids Res.
, vol.37
-
-
Lefranc, M.P.1
Giudicelli, V.2
Ginestoux, C.3
Jabado-Michaloud, J.4
Folch, G.5
Bellahcene, F.6
Wu, Y.7
Gemrot, E.8
Brochet, X.9
Lane, J.10
Regnier, L.11
Ehrenmann, F.12
Lefranc, G.13
Duroux, P.14
-
30
-
-
23244434512
-
Human immunodeficiency virus type 1 env clones from acute and early subtype B infections for standardized assessments of vaccine-elicited neutralizing antibodies
-
Li, M., F. Gao, J. R. Mascola, L. Stamatatos, V. R. Polonis, M. Koutsoukos, G. Voss, P. Goepfert, P. Gilbert, K. M. Greene, M. Bilska, D. L. Kothe, J. F. Salazar-Gonzalez, X. Wei, J. M. Decker, B. H. Hahn, and D. C. Montefiori. 2005. Human immunodeficiency virus type 1 env clones from acute and early subtype B infections for standardized assessments of vaccine-elicited neutralizing antibodies. J. Virol. 79:10108-10125.
-
(2005)
J. Virol.
, vol.79
, pp. 10108-10125
-
-
Li, M.1
Gao, F.2
Mascola, J.R.3
Stamatatos, L.4
Polonis, V.R.5
Koutsoukos, M.6
Voss, G.7
Goepfert, P.8
Gilbert, P.9
Greene, K.M.10
Bilska, M.11
Kothe, D.L.12
Salazar-Gonzalez, J.F.13
Wei, X.14
Decker, J.M.15
Hahn, B.H.16
Montefiori, D.C.17
-
31
-
-
33751224478
-
Genetic and neutralization properties of subtype C human immunodeficiency virus type 1 molecular env clones from acute and early heterosexually acquired infections in southern Africa
-
Li, M., J. F. Salazar-Gonzalez, C. A. Derdeyn, L. Morris, C. Williamson, J. E. Robinson, J. M. Decker, Y. Li, M. G. Salazar, V. R. Polonis, K. Mlisana, S. A. Karim, K. Hong, K. M. Greene, M. Bilska, J. Zhou, S. Allen, E. Chomba, J. Mulenga, C. Vwalika, F. Gao, M. Zhang, B. T. Korber, E. Hunter, B. H. Hahn, and D. C. Montefiori. 2006. Genetic and neutralization properties of subtype C human immunodeficiency virus type 1 molecular env clones from acute and early heterosexually acquired infections in southern Africa. J. Virol. 80:11776-11790.
-
(2006)
J. Virol.
, vol.80
, pp. 11776-11790
-
-
Li, M.1
Salazar-Gonzalez, J.F.2
Derdeyn, C.A.3
Morris, L.4
Williamson, C.5
Robinson, J.E.6
Decker, J.M.7
Li, Y.8
Salazar, M.G.9
Polonis, V.R.10
Mlisana, K.11
Karim, S.A.12
Hong, K.13
Greene, K.M.14
Bilska, M.15
Zhou, J.16
Allen, S.17
Chomba, E.18
Mulenga, J.19
Vwalika, C.20
Gao, F.21
Zhang, M.22
Korber, B.T.23
Hunter, E.24
Hahn, B.H.25
Montefiori, D.C.26
more..
-
32
-
-
34948854718
-
Broad HIV-1 neutralization mediated by CD4-binding site antibodies
-
Li, Y., S. A. Migueles, B. Welcher, K. Svehla, A. Phogat, M. K. Louder, X. Wu, G. M. Shaw, M. Connors, R. T. Wyatt, and J. R. Mascola. 2007. Broad HIV-1 neutralization mediated by CD4-binding site antibodies. Nat. Med. 13:1032-1034.
-
(2007)
Nat. Med.
, vol.13
, pp. 1032-1034
-
-
Li, Y.1
Migueles, S.A.2
Welcher, B.3
Svehla, K.4
Phogat, A.5
Louder, M.K.6
Wu, X.7
Shaw, G.M.8
Connors, M.9
Wyatt, R.T.10
Mascola, J.R.11
-
33
-
-
58149517700
-
Analysis of neutralization specificities in polyclonal sera derived from human immunodeficiency virus type 1-infected individuals
-
Li, Y., K. Svehla, M. K. Louder, D. Wycuff, S. Phogat, M. Tang, S. A. Migueles, X. Wu, A. Phogat, G. M. Shaw, M. Connors, J. Hoxie, J. R. Mascola, and R. Wyatt. 2009. Analysis of neutralization specificities in polyclonal sera derived from human immunodeficiency virus type 1-infected individuals. J. Virol. 83:1045-1059.
-
(2009)
J. Virol.
, vol.83
, pp. 1045-1059
-
-
Li, Y.1
Svehla, K.2
Louder, M.K.3
Wycuff, D.4
Phogat, S.5
Tang, M.6
Migueles, S.A.7
Wu, X.8
Phogat, A.9
Shaw, G.M.10
Connors, M.11
Hoxie, J.12
Mascola, J.R.13
Wyatt, R.14
-
34
-
-
34447126347
-
Crystal structure of uridine-diphospho-N-acetylglucosamine pyrophosphorylase from Candida albicans and catalytic reaction mechanism
-
Maruyama, D., Y. Nishitani, T. Nonaka, A. Kita, T. A. Fukami, T. Mio, H. Yamada-Okabe, T. Yamada-Okabe, and K. Miki. 2007. Crystal structure of uridine-diphospho-N-acetylglucosamine pyrophosphorylase from Candida albicans and catalytic reaction mechanism. J. Biol. Chem. 282:17221-17230.
-
(2007)
J. Biol. Chem.
, vol.282
, pp. 17221-17230
-
-
Maruyama, D.1
Nishitani, Y.2
Nonaka, T.3
Kita, A.4
Fukami, T.A.5
Mio, T.6
Yamada-Okabe, H.7
Yamada-Okabe, T.8
Miki, K.9
-
35
-
-
33846426122
-
Solving structures of protein complexes by molecular replacement with Phaser
-
McCoy, A. J. 2007. Solving structures of protein complexes by molecular replacement with Phaser. Acta Crystallogr. D Biol. Crystallogr. 63:32-41.
-
(2007)
Acta Crystallogr. D Biol. Crystallogr.
, vol.63
, pp. 32-41
-
-
McCoy, A.J.1
-
36
-
-
34447508216
-
Phaser crystallographic software
-
McCoy, A. J., R. W. Grosse-Kunstleve, P. D. Adams, M. D. Winn, L. C. Storoni, and R. J. Read. 2007. Phaser crystallographic software. J. Appl. Crystallogr. 40:658-674.
-
(2007)
J. Appl. Crystallogr.
, vol.40
, pp. 658-674
-
-
McCoy, A.J.1
Grosse-Kunstleve, R.W.2
Adams, P.D.3
Winn, M.D.4
Storoni, L.C.5
Read, R.J.6
-
37
-
-
0032790081
-
XtalView/Xfit - A versatile program for manipulating atomic coordinates and electron density
-
McRee, D. E. 1999. XtalView/Xfit - a versatile program for manipulating atomic coordinates and electron density. J. Struct. Biol. 125:156-165.
-
(1999)
J. Struct. Biol.
, vol.125
, pp. 156-165
-
-
McRee, D.E.1
-
38
-
-
77955010993
-
How does neutralization breadth develop in HIV infection?
-
Abstr. 013
-
Morris, L., E. Gray, P. Moore, M. Madiga, K. Mlisana, and S. A. Karim. 2010. How does neutralization breadth develop in HIV infection? Abstr. 013, p. 65. 2010 Keystone HIV Vaccine Symp. Banff, Canada.
-
(2010)
2010 Keystone HIV Vaccine Symp. Banff, Canada
, pp. 65
-
-
Morris, L.1
Gray, E.2
Moore, P.3
Madiga, M.4
Mlisana, K.5
Karim, S.A.6
-
39
-
-
70349658837
-
Philosophy of science. The coordinates of truth
-
Nabel, G. J. 2009. Philosophy of science. The coordinates of truth. Science 326:53-54.
-
(2009)
Science
, vol.326
, pp. 53-54
-
-
Nabel, G.J.1
-
40
-
-
77649132440
-
Relationship between antibody 2F5 neutralization of HIV-1 and hydrophobicity of its heavy chain third complementarity-determining region
-
Ofek, G., K. McKee, Y. Yang, Z. Y. Yang, J. Skinner, F. J. Guenaga, R. Wyatt, M. B. Zwick, G. J. Nabel, J. R. Mascola, and P. D. Kwong. 2010. Relationship between antibody 2F5 neutralization of HIV-1 and hydrophobicity of its heavy chain third complementarity-determining region. J. Virol. 84:2955-2962.
-
(2010)
J. Virol.
, vol.84
, pp. 2955-2962
-
-
Ofek, G.1
McKee, K.2
Yang, Y.3
Yang, Z.Y.4
Skinner, J.5
Guenaga, F.J.6
Wyatt, R.7
Zwick, M.B.8
Nabel, G.J.9
Mascola, J.R.10
Kwong, P.D.11
-
41
-
-
4544379899
-
Structure and mechanistic analysis of the anti-human immunodeficiency virus type 1 antibody 2F5 in complex with its gp41 epitope
-
Ofek, G., M. Tang, A. Sambor, H. Katinger, J. R. Mascola, R. Wyatt, and P. D. Kwong. 2004. Structure and mechanistic analysis of the anti-human immunodeficiency virus type 1 antibody 2F5 in complex with its gp41 epitope. J. Virol. 78:10724-10737.
-
(2004)
J. Virol.
, vol.78
, pp. 10724-10737
-
-
Ofek, G.1
Tang, M.2
Sambor, A.3
Katinger, H.4
Mascola, J.R.5
Wyatt, R.6
Kwong, P.D.7
-
42
-
-
0031059866
-
Processing of X-ray diffraction data collected in oscillation mode
-
Otwinowski, Z., and W. Minor. 1997. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276:307-326.
-
(1997)
Methods Enzymol.
, vol.276
, pp. 307-326
-
-
Otwinowski, Z.1
Minor, W.2
-
43
-
-
77954912140
-
Structure and function of broadly reactive antibody PG16 reveal an H3 subdomain that mediates potent neutralization of HIV-1
-
2 June posting date. Epub ahead of print
-
Pejchal, R., L. M. Walker, R. L. Stanfield, S. K. Phogat, W. C. Koff, P. Poignard, D. R. Burton, and I. A. Wilson. 2 June 2010, posting date. Structure and function of broadly reactive antibody PG16 reveal an H3 subdomain that mediates potent neutralization of HIV-1. Proc. Natl. Acad. Sci. U. S. A. [Epub ahead of print.]
-
(2010)
Proc. Natl. Acad. Sci. U. S. A.
-
-
Pejchal, R.1
Walker, L.M.2
Stanfield, R.L.3
Phogat, S.K.4
Koff, W.C.5
Poignard, P.6
Burton, D.R.7
Wilson, I.A.8
-
44
-
-
17944368066
-
Crystal structures of two human pyrophosphorylase isoforms in complexes with UDPGlc(Gal)NAc: Role of the alternatively spliced insert in the enzyme oligomeric assembly and active site architecture
-
Peneff, C., P. Ferrari, V. Charrier, Y. Taburet, C. Monnier, V. Zamboni, J. Winter, M. Harnois, F. Fassy, and Y. Bourne. 2001. Crystal structures of two human pyrophosphorylase isoforms in complexes with UDPGlc(Gal)NAc: role of the alternatively spliced insert in the enzyme oligomeric assembly and active site architecture. EMBO J. 20:6191-6202.
-
(2001)
EMBO J.
, vol.20
, pp. 6191-6202
-
-
Peneff, C.1
Ferrari, P.2
Charrier, V.3
Taburet, Y.4
Monnier, C.5
Zamboni, V.6
Winter, J.7
Harnois, M.8
Fassy, F.9
Bourne, Y.10
-
45
-
-
10744220076
-
Using multiple structure alignments, fast model building, and energetic analysis in fold recognition and homology modeling
-
Petrey, D., Z. Xiang, C. L. Tang, L. Xie, M. Gimpelev, T. Mitros, C. S. Soto, S. Goldsmith-Fischman, A. Kernytsky, A. Schlessinger, I. Y. Koh, E. Alexov, and B. Honig. 2003. Using multiple structure alignments, fast model building, and energetic analysis in fold recognition and homology modeling. Proteins 53(Suppl. 6):430-435.
-
(2003)
Proteins
, vol.53
, Issue.SUPPL. 6
, pp. 430-435
-
-
Petrey, D.1
Xiang, Z.2
Tang, C.L.3
Xie, L.4
Gimpelev, M.5
Mitros, T.6
Soto, C.S.7
Goldsmith-Fischman, S.8
Kernytsky, A.9
Schlessinger, A.10
Koh, I.Y.11
Alexov, E.12
Honig, B.13
-
46
-
-
0028593629
-
A broadly neutralizing human monoclonal antibody against gp41 of human immunodeficiency virus type 1
-
Purtscher, M., A. Trkola, G. Gruber, A. Buchacher, R. Predl, F. Steindl, C. Tauer, R. Berger, N. Barrett, A. Jungbauer, et al. 1994. A broadly neutralizing human monoclonal antibody against gp41 of human immunodeficiency virus type 1. AIDS Res. Hum. Retroviruses 10:1651-1658.
-
(1994)
AIDS Res. Hum. Retroviruses
, vol.10
, pp. 1651-1658
-
-
Purtscher, M.1
Trkola, A.2
Gruber, G.3
Buchacher, A.4
Predl, R.5
Steindl, F.6
Tauer, C.7
Berger, R.8
Barrett, N.9
Jungbauer, A.10
-
47
-
-
0037109074
-
Structure and function in rhodops high-level expression of rhodopsin with restricted and homogeneous N-glycosylation by a tetracycline-inducible N-acetylglucosaminyltransferase I-negative HEK293S stable mammalian cell line
-
Reeves, P. J., N. Callewaert, R. Contreras, and H. G. Khorana. 2002. Structure and function in rhodopsin: high-level expression of rhodopsin with restricted and homogeneous N-glycosylation by a tetracycline-inducible N-acetylglucosaminyltransferase I-negative HEK293S stable mammalian cell line. Proc. Natl. Acad. Sci. U. S. A. 99:13419-13424.
-
(2002)
Proc. Natl. Acad. Sci. U. S. A.
, vol.99
, pp. 13419-13424
-
-
Reeves, P.J.1
Callewaert, N.2
Contreras, R.3
Khorana, H.G.4
-
48
-
-
61749098587
-
Evolution of enzymatic activities in the enolase superfamily: Stereochemically distinct mechanisms in two families of cis, cis-muconate lactonizing enzymes
-
Sakai, A., A. A. Fedorov, E. V. Fedorov, A. M. Schnoes, M. E. Glasner, S. Brown, M. E. Rutter, K. Bain, S. Chang, T. Gheyi, J. M. Sauder, S. K. Burley, P. C. Babbitt, S. C. Almo, and J. A. Gerlt. 2009. Evolution of enzymatic activities in the enolase superfamily: stereochemically distinct mechanisms in two families of cis, cis-muconate lactonizing enzymes. Biochemistry 48:1445-1453.
-
(2009)
Biochemistry
, vol.48
, pp. 1445-1453
-
-
Sakai, A.1
Fedorov, A.A.2
Fedorov, E.V.3
Schnoes, A.M.4
Glasner, M.E.5
Brown, S.6
Rutter, M.E.7
Bain, K.8
Chang, S.9
Gheyi, T.10
Sauder, J.M.11
Burley, S.K.12
Babbitt, P.C.13
Almo, S.C.14
Gerlt, J.A.15
-
49
-
-
58149487645
-
Factors associated with the development of cross-reactive neutralizing antibodies during human immunodeficiency virus type 1 infection
-
Sather, D. N., J. Armann, L. K. Ching, A. Mavrantoni, G. Sellhorn, Z. Caldwell, X. Yu, B. Wood, S. Self, S. Kalams, and L. Stamatatos. 2009. Factors associated with the development of cross-reactive neutralizing antibodies during human immunodeficiency virus type 1 infection. J. Virol. 83:757-769.
-
(2009)
J. Virol.
, vol.83
, pp. 757-769
-
-
Sather, D.N.1
Armann, J.2
Ching, L.K.3
Mavrantoni, A.4
Sellhorn, G.5
Caldwell, Z.6
Yu, X.7
Wood, B.8
Self, S.9
Kalams, S.10
Stamatatos, L.11
-
50
-
-
63849131879
-
Broad diversity of neutralizing antibodies isolated from memory B cells in HIV-infected individuals
-
Scheid, J. F., H. Mouquet, N. Feldhahn, M. S. Seaman, K. Velinzon, J. Pietzsch, R. G. Ott, R. M. Anthony, H. Zebroski, A. Hurley, A. Phogat, B. Chakrabarti, Y. Li, M. Connors, F. Pereyra, B. D. Walker, H. Wardemann, D. Ho, R. T. Wyatt, J. R. Mascola, J. V. Ravetch, and M. C. Nussenzweig. 2009. Broad diversity of neutralizing antibodies isolated from memory B cells in HIV-infected individuals. Nature 458:636-640.
-
(2009)
Nature
, vol.458
, pp. 636-640
-
-
Scheid, J.F.1
Mouquet, H.2
Feldhahn, N.3
Seaman, M.S.4
Velinzon, K.5
Pietzsch, J.6
Ott, R.G.7
Anthony, R.M.8
Zebroski, H.9
Hurley, A.10
Phogat, A.11
Chakrabarti, B.12
Li, Y.13
Connors, M.14
Pereyra, F.15
Walker, B.D.16
Wardemann, H.17
Ho, D.18
Wyatt, R.T.19
Mascola, J.R.20
Ravetch, J.V.21
Nussenzweig, M.C.22
more..
-
51
-
-
76549125090
-
Aromatic residues at the edge of the antibody combining site facilitate viral glycoprotein recognition through membrane interactions
-
Scherer, E. M., D. P. Leaman, M. B. Zwick, A. J. McMichael, and D. R. Burton. 2010. Aromatic residues at the edge of the antibody combining site facilitate viral glycoprotein recognition through membrane interactions. Proc. Natl. Acad. Sci. U. S. A. 107:1529-1534.
-
(2010)
Proc. Natl. Acad. Sci. U. S. A.
, vol.107
, pp. 1529-1534
-
-
Scherer, E.M.1
Leaman, D.P.2
Zwick, M.B.3
McMichael, A.J.4
Burton, D.R.5
-
52
-
-
73949127978
-
Tiered categorization of a diverse panel of HIV-1 Env pseudoviruses for assessment of neutralizing antibodies
-
Seaman, M. S., H. Janes, N. Hawkins, L. E. Grandpre, C. Devoy, A. Giri, R. T. Coffey, L. Harris, B. Wood, M. G. Daniels, T. Bhattacharya, A. Lapedes, V. R. Polonis, F. E. McCutchan, P. B. Gilbert, S. G. Self, B. T. Korber, D. C. Montefiori, and J. R. Mascola. 2010. Tiered categorization of a diverse panel of HIV-1 Env pseudoviruses for assessment of neutralizing antibodies. J. Virol. 84:1439-1452.
-
(2010)
J. Virol.
, vol.84
, pp. 1439-1452
-
-
Seaman, M.S.1
Janes, H.2
Hawkins, N.3
Grandpre, L.E.4
Devoy, C.5
Giri, A.6
Coffey, R.T.7
Harris, L.8
Wood, B.9
Daniels, M.G.10
Bhattacharya, T.11
Lapedes, A.12
Polonis, V.R.13
McCutchan, F.E.14
Gilbert, P.B.15
Self, S.G.16
Korber, B.T.17
Montefiori, D.C.18
Mascola, J.R.19
-
53
-
-
67650453747
-
Human immunodeficiency virus type 1 elite neutralizers: Individuals with broad and potent neutralizing activity identified by using a high-throughput neutralization assay together with an analytical selection algorithm
-
Simek, M. D., W. Rida, F. H. Priddy, P. Pung, E. Carrow, D. S. Laufer, J. K. Lehrman, M. Boaz, T. Tarragona-Fiol, G. Miiro, J. Birungi, A. Pozniak, D. A. McPhee, O. Manigart, E. Karita, A. Inwoley, W. Jaoko, J. Dehovitz, L. G. Bekker, P. Pitisuttithum, R. Paris, L. M. Walker, P. Poignard, T. Wrin, P. E. Fast, D. R. Burton, and W. C. Koff. 2009. Human immunodeficiency virus type 1 elite neutralizers: individuals with broad and potent neutralizing activity identified by using a high-throughput neutralization assay together with an analytical selection algorithm. J. Virol. 83:7337-7348.
-
(2009)
J. Virol.
, vol.83
, pp. 7337-7348
-
-
Simek, M.D.1
Rida, W.2
Priddy, F.H.3
Pung, P.4
Carrow, E.5
Laufer, D.S.6
Lehrman, J.K.7
Boaz, M.8
Tarragona-Fiol, T.9
Miiro, G.10
Birungi, J.11
Pozniak, A.12
McPhee, D.A.13
Manigart, O.14
Karita, E.15
Inwoley, A.16
Jaoko, W.17
Dehovitz, J.18
Bekker, L.G.19
Pitisuttithum, P.20
Paris, R.21
Walker, L.M.22
Poignard, P.23
Wrin, T.24
Fast, P.E.25
Burton, D.R.26
Koff, W.C.27
more..
-
54
-
-
2442717677
-
Characterization of the human Ig heavy chain antigen binding complementarity determining region 3 using a newly developed software algorithm, JOINSOLVER
-
Souto-Carneiro, M. M., N. S. Longo, D. E. Russ, H. W. Sun, and P. E. Lipsky. 2004. Characterization of the human Ig heavy chain antigen binding complementarity determining region 3 using a newly developed software algorithm, JOINSOLVER. J. Immunol. 172:6790-6802.
-
(2004)
J. Immunol.
, vol.172
, pp. 6790-6802
-
-
Souto-Carneiro, M.M.1
Longo, N.S.2
Russ, D.E.3
Sun, H.W.4
Lipsky, P.E.5
-
56
-
-
0042282803
-
FDS: Flexible ligand and receptor docking with a continuum solvent model and soft-core energy function
-
Taylor, R. D., P. J. Jewsbury, and J. W. Essex. 2003. FDS: flexible ligand and receptor docking with a continuum solvent model and soft-core energy function. J. Comput. Chem. 24:1637-1656.
-
(2003)
J. Comput. Chem.
, vol.24
, pp. 1637-1656
-
-
Taylor, R.D.1
Jewsbury, P.J.2
Essex, J.W.3
-
57
-
-
44849132669
-
Establishing a cohort at high risk of HIV infection in South Africa: Challenges and experiences of the CAPRISA 002 acute infection study
-
van Loggerenberg, F., K. Mlisana, C. Williamson, S. C. Auld, L. Morris, C. M. Gray, Q. Abdool Karim, A. Grobler, N. Barnabas, I. Iriogbe, and S. S. Abdool Karim. 2008. Establishing a cohort at high risk of HIV infection in South Africa: challenges and experiences of the CAPRISA 002 acute infection study. PLoS One 3:e1954.
-
(2008)
PLoS One
, vol.3
-
-
Van Loggerenberg, F.1
Mlisana, K.2
Williamson, C.3
Auld, S.C.4
Morris, L.5
Gray, C.M.6
Abdool Karim, Q.7
Grobler, A.8
Barnabas, N.9
Iriogbe, I.10
Abdool Karim, S.S.11
-
58
-
-
70349887757
-
Broad and potent neutralizing antibodies from an African donor reveal a new HIV-1 vaccine target
-
Walker, L. M., S. K. Phogat, P. Y. Chan-Hui, D. Wagner, P. Phung, J. L. Goss, T. Wrin, M. D. Simek, S. Fling, J. L. Mitcham, J. K. Lehrman, F. H. Priddy, O. A. Olsen, S. M. Frey, P. W. Hammond, S. Kaminsky, T. Zamb, M. Moyle, W. C. Koff, P. Poignard, and D. R. Burton. 2009. Broad and potent neutralizing antibodies from an African donor reveal a new HIV-1 vaccine target. Science 326:285-289.
-
(2009)
Science
, vol.326
, pp. 285-289
-
-
Walker, L.M.1
Phogat, S.K.2
Chan-Hui, P.Y.3
Wagner, D.4
Phung, P.5
Goss, J.L.6
Wrin, T.7
Simek, M.D.8
Fling, S.9
Mitcham, J.L.10
Lehrman, J.K.11
Priddy, F.H.12
Olsen, O.A.13
Frey, S.M.14
Hammond, P.W.15
Kaminsky, S.16
Zamb, T.17
Moyle, M.18
Koff, W.C.19
Poignard, P.20
Burton, D.R.21
more..
-
59
-
-
0021838099
-
Neutralization of human T-lymphotropic virus type III by sera of AIDS and AIDS-risk patients
-
Weiss, R. A., P. R. Clapham, R. Cheingsong-Popov, A. G. Dalgleish, C. A. Carne, I. V. Weller, and R. S. Tedder. 1985. Neutralization of human T-lymphotropic virus type III by sera of AIDS and AIDS-risk patients. Nature 316:69-72.
-
(1985)
Nature
, vol.316
, pp. 69-72
-
-
Weiss, R.A.1
Clapham, P.R.2
Cheingsong-Popov, R.3
Dalgleish, A.G.4
Carne, C.A.5
Weller, I.V.6
Tedder, R.S.7
-
60
-
-
70449701456
-
Germline-like predecessors of broadly neutralizing antibodies lack measurable binding to HIV-1 envelope glycoproteins: Implications for evasion of immune responses and design of vaccine immunogens
-
Xiao, X., W. Chen, Y. Feng, Z. Zhu, P. Prabakaran, Y. Wang, M. Y. Zhang, N. S. Longo, and D. S. Dimitrov. 2009. Germline-like predecessors of broadly neutralizing antibodies lack measurable binding to HIV-1 envelope glycoproteins: implications for evasion of immune responses and design of vaccine immunogens. Biochem. Biophys. Res. Commun. 390:404-409.
-
(2009)
Biochem. Biophys. Res. Commun.
, vol.390
, pp. 404-409
-
-
Xiao, X.1
Chen, W.2
Feng, Y.3
Zhu, Z.4
Prabakaran, P.5
Wang, Y.6
Zhang, M.Y.7
Longo, N.S.8
Dimitrov, D.S.9
-
61
-
-
77953655567
-
Maturation pathways of cross-reactive HIV-1 neutralizing antibodies
-
Xiao, X., W. Chen, Y. Feng, and S. D. Dimitrov. 2009. Maturation pathways of cross-reactive HIV-1 neutralizing antibodies. Viruses 1:802-817.
-
(2009)
Viruses
, vol.1
, pp. 802-817
-
-
Xiao, X.1
Chen, W.2
Feng, Y.3
Dimitrov, S.D.4
-
62
-
-
17644392830
-
TM-align: A protein structure alignment algorithm based on the TM-score
-
Zhang, Y., and J. Skolnick. 2005. TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res. 33:2302-2309.
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. 2302-2309
-
-
Zhang, Y.1
Skolnick, J.2
-
63
-
-
0036838311
-
Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction
-
Zhou, H. Y., and Y. Q. Zhou. 2002. Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction. Protein Sci. 11:2714-2726.
-
(2002)
Protein Sci.
, vol.11
, pp. 2714-2726
-
-
Zhou, H.Y.1
Zhou, Y.Q.2
-
64
-
-
33847101745
-
Structural definition of a conserved neutralization epitope on HIV-1 gp120
-
Zhou, T., L. Xu, B. Dey, A. J. Hessell, D. Van Ryk, S. H. Xiang, X. Yang, M. Y. Zhang, M. B. Zwick, J. Arthos, D. R. Burton, D. S. Dimitrov, J. Sodroski, R. Wyatt, G. J. Nabel, and P. D. Kwong. 2007. Structural definition of a conserved neutralization epitope on HIV-1 gp120. Nature 445:732-737.
-
(2007)
Nature
, vol.445
, pp. 732-737
-
-
Zhou, T.1
Xu, L.2
Dey, B.3
Hessell, A.J.4
Van Ryk, D.5
Xiang, S.H.6
Yang, X.7
Zhang, M.Y.8
Zwick, M.B.9
Arthos, J.10
Burton, D.R.11
Dimitrov, D.S.12
Sodroski, J.13
Wyatt, R.14
Nabel, G.J.15
Kwong, P.D.16
-
65
-
-
77649336168
-
Building and refining protein models within cryo-electron microscopy density maps based on homology modeling and multiscale structure refinement
-
Zhu, J., L. Cheng, Q. Fang, Z. H. Zhou, and B. Honig. 2010. Building and refining protein models within cryo-electron microscopy density maps based on homology modeling and multiscale structure refinement. J. Mol. Biol. 397:835-851.
-
(2010)
J. Mol. Biol.
, vol.397
, pp. 835-851
-
-
Zhu, J.1
Cheng, L.2
Fang, Q.3
Zhou, Z.H.4
Honig, B.5
|