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Document 42. Esnouf R, Ren J, Ross R, Jones Y, Stammers D, Stuart D. Mechanism of inhibition of HIV-1 reverse transcriptase by non-nucleoside inhibitors. Nature Struct Biol 1995; 2:303–308. 43. Hsiou Y, Ding J, Das K, Clark AD Jr., Hughes SH, Arnold E. Structure of unliganded HIV-1 reverse transcriptase at 2.7 Å resolution: implications of conformational changes for polymerization and inhibition mechanisms. Structure 1996; 4:853–860. 44. Unge T, Knight S, Bhikhabhai R, Lovgren S, Dauter Z, Wilson K, et al. 2.2 Å resolution structure of the amino-terminal half of HIV-1 reverse transcriptase (fingers and palm subdomains). Structure 1994; 2:953–961. http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_73.html (2 of 2) [4/5/2004 4:53:09 PM]
Document 45. Majumadar C, Abbotts J, Broder S, Wilson SH. Studies on the mechanism of human immunodeficiency virus reverse transcriptase: Steady-state kinetics, processivity and polynucleotide inhibiton. J Biol Chem 1988; 263:15657–15665. 46. Kati WM, Johnson KA, Jerva LF, Anderson KS. Mechanism and fidelity of HIV reverse transcriptase. J Biol Chem 1992; 267:25988–25997. 47. Balzarini J, Herdewijn P, De Clercq E. Differential patterns of intracellular metabolism of 2',3'didehydro-2',3'-dideoxthymidine and 3'-azido-2',3'- dideoxythymidine: two potent anti-human immunodeficiency virus compounds. J Biol Chem 1989; 264:6127–6133. 48. Balzarini J, De Clercq E. 5' -Phosphoribosyl 1-pyrophosphate synthetase converts the acyclic nucleoside phosphonates 9-(3-hydroxy-2-phosphonyl-methoxypropyl) adenine and 9-(2phosphonylmethoxyethyl)adenine directly to their antivirally active diphosphate derivatives. J Biol Chem 1991; 266:8686–8689. 49. Merta AI, Votruba J, Jindrich J, Holy A, Cihlar T, Rosenberg I, et al. Phosphorylation of 9-(2phosphonylmethoxyethyl)adenine and (S)-9-(3-fluoro-2-phosphonylmethoxypropyl)adenine by AMP (dAMP) kinase from L1210 cells. Biochem Pharmacol 1992; 44:2067–2077. 50. De Clercq E. Broad spectrum anti-DNA virus and anti-retrovirus activity of phosphonylmethoxyalkyl-purines and -pyrimidines. Biochem Pharmacol 1991; 42:963–972. 51. Balzarini J, Hao Z, Herdewijn P, Johns DG, De Clercq E. Intracellular metabolism and mechanism of anti-retrovirus action of 9-(2-phosphonyl-methoxyethyl) adenine, a potent anti-human immunodeficiency virus compound. Proc Natl Acad Sci USA 1991; 88:1499–1503. Page 74 52. Balzarini J, Holy A, Jindrich J, Dvorakova H, Hao Z, Snoeck R, et al. 9-[(2RS)-3- fluoro-2phosphonylmethoxyethyl] derivatives of purines: a class of highly selective antiretroviral agents in vitro and in vivo. Proc Natl Acad Sci USA 1991; 88:4961–4965. 53. Patel PH, Jacobo-Molina A, Ding J, Tantillo C, Clark AD Jr., Raag R, et al. Insights into DNA polymerization mechanisms from structure and function analysis of HIV-1 reverse transcriptase. Biochemistry 1995; 34:5351–5363. 54. Boyer PL, Tantillo C, Jacobo-Molina A, Nanni RG, Ding J, Arnold E, et al. The sensitivity of wildtype human immunodeficiency virus type 1 reverse transcriptase to dideoxynucleotides depends on template length; the sensitivity of drug-resistant mutants does not. Proc Natl Acad Sci USA 1994; 91:4882–4886. 55. Kellam P, Boucher CA, Larder BA. Fifth mutation in human immunodeficiency virus type 1 reverse transcriptase contributes to the development of high-level resistance to zidovudine. Proc Natl Acad Sci USA 1992; 89:1934–1938. http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_74.html (1 of 2) [4/5/2004 4:53:11 PM]
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Structure-based Drug Design 14 Stru
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Document Page 33 sustained in many
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Page 51 and 52: Document 2 Structural Studies of HI
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Page 57 and 58: Document Figure Continued Page 45 r
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Page 63 and 64: Document monophosphate analogs whic
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Page 67 and 68: Document Page 54 Table 2) [12,54].
Page 69 and 70: Document Page 56 It is also attract
Page 71 and 72: Document Table 3 HIV-1 RT Amino Aci
Page 73 and 74: Document ever, once an NNRTI is bou
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Page 77 and 78: Document Page 63 most of the amino
Page 79 and 80: Document Page 65 cal properties of
Page 81 and 82: Document Page 67 Biochemical data s
Page 83 and 84: Document Page 69 determining the me
Page 85 and 86: Document Chris Tantillo. The work i
Page 87 and 88: Document Page 72 16. Goldman ME, Nu
Page 89: Document 30. Coffin JM. HIV populat
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Page 95 and 96: Document 75. Ring CS, Sun E, McKerr
Page 97 and 98: Document 89. Hughes SH, Arnold E, H
Page 99 and 100: Document 106. Cirino NM, Cameron CE
Page 101 and 102: Document 122. Marshall WS, Beaton G
Page 103 and 104: Document dine) and didanosine (dide
Page 105 and 106: Document 149. Craig JC, Duncan IB,
Page 107 and 108: Document 163. Lacey SF, Larder BA.
Page 109 and 110: Document Figure 1 Retroviral lifecy
Page 111 and 112: Document Figure 2 In vivo reactions
Page 113 and 114: Document Page 88 transfer (Figure 3
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Page 117 and 118: Document Page 92 The role of the N-
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Page 121 and 122: Document Page 96 region in the HIV-
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Page 127 and 128: Document Page 101 crystallized unde
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Page 131 and 132: Document proposed mechanisms. For e
Page 133 and 134: Document Page 106 on the same ring
Page 135 and 136: Document Page 108 mulate during tre
Page 137 and 138: Document when metals are bound. Fin
Page 139 and 140: Document cubation of phosphotyrosin
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Document 4. Vink C, Plasterk RHA. T
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Document 65. Gallay P, Swingler S,
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Document 4 Bradykinin Receptor Anta
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Document Page 121 Nearly all cells
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Document Page 125 binding site on t
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Document Page 127 The des-Arg 9 for
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Document receptor, it has not yet b
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Document Page 133 This initial stag
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Document Page 135 might be jointly
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Document Page 137 observed for the
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Document Figure 6 Rat and human B2
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Document Page 141 receptor with int
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Document Figure 9 Composition of te
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Document 16. Martorana PA, Kettenba
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Document 39. Mavunkel BJ, Lu Z, Kyl
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Document B. Pharmacology Figure 1 T
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Document We determined the structur
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Document Figure 3 Previously known
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Document large solvent channels and
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Document IV. Drug Design Progressio
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Document position eight from formin
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Document Table 1 Inhibition Data fo
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Document Page 166 As predicated, th
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Document References 1. Parks RE Jr.
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Document 17. Ealick SE, Rule SA, Ca
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Document 6 Structural Implications
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Document Figure 1 A ribbon model of
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Document Page 176 0.43 Å) as the c
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Document Page 182 (SAR) model. The
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Document IX. S2' Interactions Page
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Document 7 Structure—Function Rel
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Document Important for the validity
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Document Figure 4 Amino acids impor
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Document III. Results and Discussio
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Document Page 202 269, and valine-2
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Document Figure 6 Structure of α h
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Document Page 205 enzyme and of phe
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Document Page 207 sure and the acti
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Document 13. Wilson RC, Krozowski Z
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Document 29. Baker ME. Genealogy of
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Document 31. Kettner C, Shaw E. D-P
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Document Table 2 Naturally Occurrin
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Document 12 Polypeptide Modulators
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Document A. Chemical Modification P
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Document C. Specificity Figure 4 Th
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Document IV. Rational Drug Design F
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Document 2. Blundell TL, Cooper J,
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Document 17. Szelke M. Chemistry of
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Document Table 1 Trypanosomal Targe
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Document 16 Progress in the Design
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Document Page 398 with growth hormo
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Document All effects of the IL-1 fa
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Document Page 405 strands constitut
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Document Page 412 ture is unlike ot
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Document Page 416 positions of the
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Document Figure 11 Functional resid
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Document Figure 13 The identified p
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Document B. Interleukin-1 Receptor
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Document Page 425 Antinflammatory D
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Document Page 427 These aromatic di
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Document 5. Dinarello CA. On the Bi
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Document 21. Seckinger P, Lowenthal
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Document 39. Saurat JH, Schfferli J
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Document receptor antagonist into a
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Document 74. Bender PE, Lee JC., ed
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Document 102. Machin PJ, Osbond JM,
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Document 17 Structure and Functiona
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Document Table 1 Approval Indicatio
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Document Page 438 proteins. One pot
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Document II. Type IFNs A great deal
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Document Page 441 sequence of the m
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Document Page 443 that allowed for
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Document Figure 4 Stereo view of IF
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Document Figure 5 Velcro-key model
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Document Figure 6 Proposed receptor
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Document Page 451 with the cytoplas
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Document for directed subcellular t
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Document 13. Stewart HJ, McCann SHE
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Document 33. Szente BE, Johnson HM.
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Document 47. Igarashi K, Garotta G,
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Document Figure 1 A schematic diagr
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Document Page 462 strains of influe
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Document Page 464 could not again b
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Document Figure 3 (a) A MOLSCRIPT [
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Document B. Protein Structure Page
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Document Figure 5 (a) Stereo image
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Document Page 471 molecules in the
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Document hydroxy, and 6 Neu5Ac2en -
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Document Figure 8 Stereo image of t
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Document Page 476 nM, respectively.
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Document Page 478 lished—was asso
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Document VI. Conclusion Page 480 It
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Document 21. Both GW, Sleigh MJ, Co
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Document 40. Drzenick R, Frank H, R
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Document 45. Varghese JN, Laver WG,
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Document 64. Ward CW, Elleman TC, A
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Document 80. Suzuki Y, Sato K, Kiso
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Document Page 486 95. Ryan DM, Tice
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Document Page 488 against most of t
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Document A. The Canyon Page 491 The
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Document Subsequent studies have sh
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Document Page 495 of the RNA and pr
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Document Figure 4 A ribbon diagram
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Document Figure 5 Some compounds wh
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Document Figure 7 HRV14 VP1 hydroph
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Document C. Structure-Activity Rela
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Document Figure 10 Possible hydroge
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Document Page 514 sis. Large number
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Document conformational transition
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Document Page 518 The differences b
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Document Page 527 function. Iterati
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Document 10. Bobbyer DNA, Goodford
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Document Figure 32 PTP and PTB 3D s
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Document Acknowledgments Page 620 I
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Document 18. Sawyer TK. In: Peptide
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Document MA, Welch KM, Hallak H, Ta
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Document 97; (e) Fujii I, Nakamura
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Document Med Biol 1991; 306:9-21; (
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Document Page 629 ML, Clare M, Decr
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Document Page 630 177. (a) Bode W,
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Document Page 631 197. Musil D, Zuc
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Document son AH, Drummond AH, Huxle
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Document Cyclotheonamide A (CtA), 2
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Document D ddI, 152 tumour necrosis
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Document antistasin peptides, 281 c
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Document fragment-based programs, 5
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Document [Human immunodeficiency vi
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Document Kininogen, 119 high molecu
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Document RT inhibitor, 41, 56 Nonpe
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Document Phosphoglycerate kinase (P
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Document [Protease targets] serinyl
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