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Document While the x-ray structure of antistasin has not been reported, it is known that a Factor-Xa-induced cleavage occurs between Arg 34 and Val 35 suggesting this peptide loop conforms to the conformationally rigid substratelike conformation suggested by other known protein inhibitors of serine proteases [55]. A hallmark of this mode of inhibition is the rigid structure around the cleaved http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_271.html (2 of 2) [4/5/2004 5:12:47 PM]
Document Figure 5 Predicted secondary structure of tissue factor pathway inhibitor (TFPI) showing the Factor Xa and Factor VIIa inhibitory domains. The arrows point to the P1 sites. Page 272 bond, often imposed by cysteine crosslinks constraining the two ends of the cleavage site to be in close proximity even after cleavage [47]. Antistasin has cysteines at the P2(Cys 33) and P'3 (Cys 37) positions. C. Tick Anticoagulant Peptide (TAP) The tick anticoagulant peptide (TAP) is a 60-amino-acid polypeptide isolated from the soft tick Ornithodorus Moubata and is a potent (K i = 2–200 pM) and selective inhibitor of Factor Xa, both as the free enzyme and in the prothrombinase complex [13]. The TAP anticoagulant does not inhibit trypsin or other trypsinlike serine proteases and, importantly, is not cleaved by Factor Xa. The mechanism by which TAP inhibits Factor Xa appears to be unique and it apparently does not utilize the substratelike binding modes characteristic of antistasin and the Kunitz inhibitors. Mutagenesis studies have shown that the primary interaction of TAP with Factor Xa occurs at the N-terminous where Arg 3 appears to play a key role [56]. The solution structure of TAP has been deter- http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_272.html [4/5/2004 5:12:58 PM]
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Structure-based Drug Design 14 Stru
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Document TF—transframe, PR—prot
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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 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 Figure 6 (a) The pocket of
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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 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 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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Page 285 and 286: Document Figure 3 C α trace of the
Page 287 and 288: Document Figure 4 Surface represent
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Page 291 and 292: Document Figure 7 Stereo of zopolre
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Page 295 and 296: Document This method was used to sc
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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 319 and 320: Document balance its pro- and antic
Page 321 and 322: Document Page 263 15. Tabernero L,
Page 323 and 324: Document 31. Kettner C, Shaw E. D-P
Page 325 and 326: Document Figure 1 The coagulation c
Page 327 and 328: Document Figure 2 Factor Xa structu
Page 329 and 330: Document Table 2 Naturally Occurrin
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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
Page 345 and 346: Document Figure 12 Modeled fit of S
Page 347 and 348: Document Page 285 number of x-ray s
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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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Page 373 and 374: Document A. Chemical Modification P
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Document Page 314 anemone toxins an
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Document 13 Rational Design of Reni
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Document Page 327 this analog inter
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Document plasma. This may arise fro
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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 2 The reaction cata
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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 Figure 10 Structures of so
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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 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 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 Page 405 strands constitut
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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 425 Antinflammatory D
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Document Page 427 These aromatic di
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Document 21. Seckinger P, Lowenthal
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Document 39. Saurat JH, Schfferli J
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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 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 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 17. Zuckermann RN, Martin
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Document 21 Structure-Based Combina
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Document Page 545 protein binding s
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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 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 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 (Ser/Thr) peptide 2.9 Å 2
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Document Page 617 Val (131) showed
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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 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 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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