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Document 18. Johnson MS, McClure MA, Feng D–F, Gray J, Doolittle RF. Computer analysis of retroviral pol genes: Assignment of enzymatic functions to specific sequences and homologies with nonviral enzymes. Proc Natl Acad Sci USA 1986; 83:7648–7652. 19. Engelman A, Craigie R. Identification of conserved amino acid residues critical for human immunodeficiency virus type 1 integrase function in vitro. J Virol 1992; 66:6361–6369. 20. Van Gent DC, Oude Groeneger AAM, Plasterk RHA. Mutational analysis of the integrase protein of human immunodeficiency virus type 2. Proc Natl Acad Sci USA 1992; 89:9598–9602. http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_114.html (2 of 2) [4/5/2004 4:52:29 PM]
Document Page 115 21. Kulkosky J, Jones KS, Katz RA, Mack JPG, Skalka AM. Residues critical for retroviral integrative recombination in a region that is highly conserved among retroviral/retrotransposon integrases and bacterial insertion sequence transposases. Mol Cell Biol 1992; 12:2331–2338. 22. Bushman FD, Engelman A, Palmer I, Wingfield P, Craigie R. Domains of the integrase protein of human immunodeficiency virus type 1 responsible for polynucleotidyl transfer and zinc binding. Proc Natl Acad Sci USA 1993; 90:3428–3432. 23. Beese LS, Steitz TA. Structural basis for the 3'-5' exonuclease activity of Escherichia coli DNA polymerase I: a two metal ion mechanism. EMBO J 1991; 10:25–33. 24. Woerner AM, Marcus-Sekura CJ. Characterization of a DNA binding domain in the C-terminus of HIV-1 integrase <strong>by</strong> deletion mutagenesis. Nucl Acids Res 1993; 21:3507–3511. 25. Vink C, Oude Groeneger AAM, Plasterk RHA. Identification of the catalytic and DNA-binding region of the human immunodeficiency virus type 1 integrase protein. Nucl Acids Res 1993; 21:1419–1425. 26. Puras Lutzke RA, Vink C, Plasterk RHA. Characterization of the minimal DNA-binding domain of the HIV integrase protein. Nucl Acids Res 1994; 22:4125–4131. 27. Drelich M, Wilhelm R, Mous J. Identification of amino acid residues critical for endonuclease and integration activities of HIV-1 IN protein in vitro. Virol 1992; 188:459–468. 28. Lodi PJ, Ernst JA, Kuszewski J, Hickman AB, Engelman A, Craigie R, Clore GM, Gronenborn AM. Solution structure of the DNA binding domain of HIV-1 integrase. Biochem 1995; 34:9826–9833. 29. Eijkelenboom APAM, Puras Lutzke RA, Boelens R, Plasterk RHA, Kaptein R, Hard K. The DNAbinding domain of HIV-1 integrase has an SH3-like fold. Nature Struct Biol 1995; 2:807–810. 30. Haugan IR, Nilsen BM, Worland S, Olsen L, Helland DE. Characterization of the DNA-binding activity of HIV-1 integrase using a filter binding assay. Biochem Biophys Res Commun 1995; 217:802–810. 31. Burke CJ, Sanyal G, Bruner MW, Ryan JA, LaFemina RL, Robbins HL, Zeft AS, Middaugh CR, Cordingley MG. Structural implications of spectroscopic characterization of a putative zinc finger peptide from HIV-1 integrase. J Biol Chem 1992; 267:9639–9644. 32. Bushman FD, Wang B. Rous sarcoma virus integrase protein: Mapping functions for catalysis and substrate binding. J Virol 1994; 68:2215–2223. 33. Engelman A, Hickman AB, Craigie R. The core and carboxyl-terminal domains of the integrase protein of human immunodeficiency virus type 1 each contribute to nonspecific DNA binding. J Virol 1994; 68:5911–5917. http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_115.html (1 of 2) [4/5/2004 4:52:31 PM]
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netLibrary - eBook Summary Universi
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Structure-based Drug Design 14 Stru
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Document 22. Krausslich HG, Ingraha
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Document 47. Tummino PJ, Ferguson D
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Document 60. Condra JH, Schleif WA,
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Document 74. Reddy RM, Varney MD, K
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Document 2 Structural Studies of HI
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Document Figure 1 (a) Chemical stru
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Document dine (3TC), and 2',3'-dide
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Document Figure Continued Page 45 r
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Document monophosphate analogs whic
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Document Analysis of various HIV-1
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Document Page 54 Table 2) [12,54].
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Document Page 56 It is also attract
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Document Table 3 HIV-1 RT Amino Aci
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Document ever, once an NNRTI is bou
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Document Page 61 now clear that the
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Document Page 63 most of the amino
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Document Page 65 cal properties of
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Document Page 67 Biochemical data s
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Document Page 69 determining the me
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Document Chris Tantillo. The work i
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Document Page 72 16. Goldman ME, Nu
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Document 30. Coffin JM. HIV populat
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Page 93 and 94: Document reverse transcriptase inhi
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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
Page 129 and 130: Document Figure 8 Molscript stereo
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
Page 141: Document 4. Vink C, Plasterk RHA. T
Page 145 and 146: Document 44. Cushman M, Sherman P.
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Page 149 and 150: Document 4 Bradykinin Receptor Anta
Page 151 and 152: Document Page 121 Nearly all cells
Page 153 and 154: Document Page 123 were poorly satis
Page 155 and 156: Document Page 125 binding site on t
Page 157 and 158: Document Page 127 The des-Arg 9 for
Page 159 and 160: Document Page 129 tolerated by the
Page 161 and 162: Document receptor, it has not yet b
Page 163 and 164: Document Page 133 This initial stag
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Page 167 and 168: Document Page 137 observed for the
Page 169 and 170: Document Figure 6 Rat and human B2
Page 171 and 172: Document Page 141 receptor with int
Page 175 and 176: Document Figure 9 Composition of te
Page 179 and 180: Document 16. Martorana PA, Kettenba
Page 181 and 182: Document 39. Mavunkel BJ, Lu Z, Kyl
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Page 187 and 188: Document We determined the structur
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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 178 studies show that
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Document Figure 5 (a) A cut away vi
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Document Page 182 (SAR) model. The
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Document IX. S2' Interactions Page
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Document Figure 6 (a) The pocket of
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Document 5. Willenbrock F, Murphy G
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Document 20. Murphy G, Docherty AJP
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Document Page 189 36. Bode W, Reine
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Document 7 Structure—Function Rel
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Document Figure 1 Reactions catalyz
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Document Figure 2 Structure of lico
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Document Figure 3 (Continued) Page
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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 46. Ribas dePoplana L, Fot
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Document Page 214 viruses. Specific
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Document Page 218 The catalytic loo
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Document Figure 3 (a) Ternary compl
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Document Figure 5 (a) Staurosporine
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Document protein kinase core is ess
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Document 10. Knighton DR, Zheng J-H
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Document 24. Madhusudan Xuong N-H,
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Document 9 Structural Studies of Al
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Document diverse ARIs have been sho
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Document Figure 3 C α trace of the
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Document Figure 4 Surface represent
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Document Figure 7 Stereo of zopolre
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Document B. Structures Figure 8 Seq
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Document This method was used to sc
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Document 18. Wilson DK, Tarle I, Pe
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Document 35. Pailhoux EA, Martinez
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Document 10 Structure-Based Design
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Document Cyclotheonamide A (CtA), a
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Document Page 256 The discovery pro
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Document balance its pro- and antic
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Document Page 263 15. Tabernero L,
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Document 31. Kettner C, Shaw E. D-P
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Document Figure 1 The coagulation c
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Document Figure 2 Factor Xa structu
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Document Table 2 Naturally Occurrin
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Document Table 3 Active Site Sequen
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Document Figure 5 Predicted seconda
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Document Lys in the P1 position is
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Document Page 276 In both cases the
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Document Page 278 The n=3 chain len
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Document Figure 10 Proposed model o
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Document Figure 11 dArg-ATS 32-38 m
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Document Page 285 number of x-ray s
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Document Page 288 Additionally, the
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Document 36. Leytus SP, Chung DW, K
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Document 54. Broze Jr GJ, Girard TJ
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Document 12 Polypeptide Modulators
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Document Page 297 whereas, calcium
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Document Figure 2 Amino acid sequen
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Document Page 301 domains contribut
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Document Figure 5 Stereo views of 2
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Document A. Chemical Modification P
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Document Page 307 (the exception is
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Document Page 309 site 3 on the sod
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Document Page 314 anemone toxins an
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Document 60. Pennington MW, Zadenbe
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Document 13 Rational Design of Reni
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Document Page 323 been suggested th
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Document Page 327 this analog inter
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Document C. Specificity Figure 4 Th
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Document Figure 5 The S 3 specifici
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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 34. Rosenberg SH, Plattner
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Document 48. Powers JC, Harley AD,
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Document Page 343 14 Structural Asp
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Document Figure 4 Amino acid sequen
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Document Figure 8 The catalytic mac
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Document Figure 10 Structures of so
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Document From quantitative structur
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Document Page 355 with the tryptoph
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Document Figure 14 The energy profi
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Document Page 359 easily reach the
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Document Table 1 Trypanosomal Targe
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Document Table 2 Three-Dimensional
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Document Figure 2 Glycolysis in blo
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Document II. Three Glycolytic Enzym
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Document Figure 6 Stereoview of NAD
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Document 5-Methoxytryptamine 19.0 9
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Document Figure 12 Predicted bindin
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Document Page 388 nosine proved to
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Document 15. Carter NS, Fairlamb AH
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Document 30. Kim H, Feil I, Verlind
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Document 49. Michels PAM, Hannaert
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Document 65. João HC, Williams RJP
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Document 84. Verlinde CLMJ, Hol WGJ
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Document 16 Progress in the Design
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Document Table 1 Known Three-Dimens
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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 Figure 2 Structural alignm
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Document Page 405 strands constitut
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Document Figure 4 (a) Stereo diagra
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Document Figure 6 (a) Stereo diagra
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Document Figure 7 (a) Superposition
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Document Page 412 ture is unlike ot
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Document Figure 10 Schematic diagra
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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 423 American Home Pro
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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 Hydrophobicity Requirement
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Document Figure 9 A solvent-accessi
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Document accommodate a variety of d
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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 10. Mast EE, Harmon MW, Gr
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Document 25. Arnold E, Rossmann MG.
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Document 44. Argos P, Rossmann MG,
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Document 63. Rozhon E, Cox S, Buont
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Document 81. Diana GD, McKinlay MA,
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Document 20 The Integration of Stru
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Document Page 527 function. Iterati
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Document Figure 3 Generation of com
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Document Page 530 screen. For examp
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Document ciency of drug discovery (
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Document Page 533 the reactions are
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Document Page 535 by factoring in a
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Document Page 537 ries, holds the p
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Document 17. Zuckermann RN, Martin
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Document 34. Fei Y-J, Kanai Y, Nuss
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Document 21 Structure-Based Combina
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Document Page 545 protein binding s
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Document Lists of Bonding Fragment
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Document Figure 8 Minimized structu
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Document Page 555 N-acylpyrrolidine
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Document 10. Bobbyer DNA, Goodford
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Document structure. 2. Ligand probe
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Document 30. O'Shea EK, Rutkowski R
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Document 22 Peptidomimetic and Nonp
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Document Figure 1 Examples of nativ
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Document B. Peptidomimetic Drugs: C
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Document Figure 4 Backbone amide bo
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Document 12640-0567a.gif Figure 6 C
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Document Page 569 molecule. A nonco
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Document Figure 22 Protease 3D stru
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Document Page 601 inhibitors 100 [1
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Document Page 603 hydroxymethyl sub
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Document Page 607 scopic studies pr
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Document (Ser/Thr) peptide 2.9 Å 2
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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 Page 622 Fukuroda T, Fukam
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Document Page 623 53. Bird J, Harpe
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Document 78. Rodriguez M, Crosby R,
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Document MA, Welch KM, Hallak H, Ta
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Document Page 626 SJ, Ogden RC, Red
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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 236. (a) Marshall MS. TIBS
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Document 274. (a) Kavanaugh WM, Wil
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Document replacements, 563-565 1-am
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Document inhibitor binding, 323, 33
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Document site, 52, 55, 61 triad, 24
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Document factors, 247 Combination t
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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 overview, 103-104, 108-109
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Document [Inhibitors] 2-((3,4-dihyd
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Document antagonistic activity, 416
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Document [Interleukin-1] homology w
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Document Kininogen, 119 high molecu
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Document Matrix-metalloproteinase (
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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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