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Document 12. Wu T-P, Yee V, Tulinsky A, Chrusciel R, Nakanishi H, Shen R, Priebe C, Kahn M. The structure of a designed peptidomimetic inhibitor complex of α-thrombin. Protein Engineering 1993; 5:471–478. 13. Obst U, Gramlich V, Diederich F, Weber L, Banner DW. Design of novel, nonpeptidic thrombin inhibitors and structure of a thrombin-inhibitor complex. Angew Chem Int Ed Engl 1995; 34:1739. 14. Iwanowicz EJ, Lau WF, Lin J, Roberts DGM, Seiler SM. Retro-binding tripeptide thrombin active inhibitors: discovery, synthesis and molecular modeling. J Med Chem 1994; 37:2122–2124. http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_262.html (2 of 2) [4/5/2004 5:11:34 PM]
Document Page 263 15. Tabernero L, Chang CÁ, Ohringer SL, Lau WF, Iwanowicz EJ, Han W-C, Wang T, Seiler S, Roberts D, Sack JS. Structure of a retro-binding peptide inhibitor complexed with human α-thrombin. J Mol Biol 1995; 246:14–20. 16. Maryanoff BE, Qiu Z, Padmanabhan KP, Tulinsky A, Almond HR, Andrade-Gordon P, Greco M, Kauffman J, Nicolaou KC, Liu A, Brung P, Fusetani N. Molecular basis for the inhibition of human αthrombin by the macrocyclic peptide cyclotheonamide A. Natl Academy Sci USA 1993; 90:8048–8052. 17. Hilpert K, Ackermann J, Banner DW, Gast A, Gubernator K, Hadvary P, Labler L, Muller K, Schmid G, Tschopp T, Van de Waterbeemd H. Design and synthesis of potent and highly selective thrombin inhibitors. J Med Chem 1994; 37:3889–3901. 18. Rydel TJ, Tulinsky A, Bode W, Ravichandran KG, Huber R, Roitsch R, Fenton JW, II. The structure of a complex of recombinant hirudin and human α-thrombin. Science 1990; 249:277–280. 19. Grutter MG, Priestle JP, Rahuel J, Grossenbacher H, Bode W, Hofsteenge J, Stone SR. Crystal structure of the thrombin-hirudin complex: a novel mode of serine protease inhibitor. EMBO J 1990; 9:2361–2365. 20. Rydel TJ, Tulinsky A, Bode W, Huber R. Refined structure of the hirudin-thrombin complex. J Mol Biol 1991; 221:583–601. 21. Maraganore JM, Bourdon P, Jablonski J, Ramachandran KL, Fenton JW, II. Design and characterization of hirulogs: a novel class of bivalent peptide inhibitors of thrombin. Biochemistry 1990; 29:7095–7101. 22. DiMaio J, Gibbs B, Munn D, Lefebvre J, Ni F, Konishi Y. Bifunctional thrombin inhibitors based on the sequence of hirudin. J Biol Chem 1990; 265:21698–21703. 23. Kettner C, Shaw E. D-Phe-Pro-Arg CH 2C1—A selective affinity label for thrombin. Thromb Res 1979; 14:969–973. 24. DiMaio J, Ni F, Gibbs B, Konishi Y. A new class of potent thrombin inhibitors that incorporates a scissile pseudopeptide bond. FEBS 1991; 282:47–52. 25. DiMaio J, Gibbs B, Lefebvre J, Konishi Y, Munn D, Yue SY. Synthesis of a homologous series of ketomethylene arginyl pseudodipeptides and application to low molecular weight hirudin-like thrombin inhibitors. J Med Chem 1992; 35:3331–3341. 26. Zdanov A, Wu S, DiMaio Y, Konishi Y, Li Y, Wu X, Edwards B, Martin P, Cygler M. Crystal structure of the complex of human α-thrombin and nonhydrolyzable bifunctional inhibitors, hirutonin-2 and hirutonin-6. PROTEINS: Structure, Function and Genetics 1993; 17:252–265. http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_263.html (1 of 2) [4/5/2004 5:11:39 PM]
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netLibrary - eBook Summary Universi
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Structure-based Drug Design 14 Stru
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Document compounds that utilize sim
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Document Figure 7 Cartoon represent
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Document Figure 8 Cartoon represent
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Document Page 33 sustained in many
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Document 8. Kaplan AH, Zack JA, Kni
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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 Figure 2 Ribbon diagrams o
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Document Figure 3 Overall structure
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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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Document 45. Majumadar C, Abbotts J
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Document reverse transcriptase inhi
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Document 75. Ring CS, Sun E, McKerr
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Document 89. Hughes SH, Arnold E, H
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Document 106. Cirino NM, Cameron CE
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Document 122. Marshall WS, Beaton G
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Document dine) and didanosine (dide
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Document 149. Craig JC, Duncan IB,
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Document 163. Lacey SF, Larder BA.
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Document Figure 1 Retroviral lifecy
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Document Figure 2 In vivo reactions
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Document Page 88 transfer (Figure 3
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Document Page 92 The role of the N-
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Document Figure 6 Molscript stereo
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Document Page 96 region in the HIV-
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Document day junction resolving enz
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Document -62° for HIV-1 integrase,
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Document Page 101 crystallized unde
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Document Figure 8 Molscript stereo
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Document proposed mechanisms. For e
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Document Page 106 on the same ring
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Document Page 108 mulate during tre
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Document when metals are bound. Fin
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Document cubation of phosphotyrosin
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Document 4. Vink C, Plasterk RHA. T
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Document Page 115 21. Kulkosky J, J
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Document 44. Cushman M, Sherman P.
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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 123 were poorly satis
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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 Page 129 tolerated by the
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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 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 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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Page 275 and 276: Document protein kinase core is ess
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Page 311 and 312: Document Cyclotheonamide A (CtA), a
Page 313 and 314: Document Page 256 The discovery pro
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Page 331 and 332: Document Table 3 Active Site Sequen
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Page 335 and 336: Document Lys in the P1 position is
Page 337 and 338: Document Page 276 In both cases the
Page 339 and 340: Document Page 278 The n=3 chain len
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Page 343 and 344: Document Figure 11 dArg-ATS 32-38 m
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Page 363 and 364: Document 12 Polypeptide Modulators
Page 365 and 366: Document Page 297 whereas, calcium
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Document A. Chemical Modification P
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Document Page 309 site 3 on the sod
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Document 13 Rational Design of Reni
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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 5 Schematic stereo
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Document Figure 8 The catalytic mac
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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 4 Stereoview of sup
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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 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 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 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 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 Page 527 function. Iterati
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Document Page 530 screen. For examp
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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 Page 545 protein binding s
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Document Page 555 N-acylpyrrolidine
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Document 10. Bobbyer DNA, Goodford
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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 B. Peptidomimetic Drugs: C
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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 605 For other serinyl
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Document Page 607 scopic studies pr
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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 78. Rodriguez M, Crosby R,
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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 236. (a) Marshall MS. TIBS
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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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