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Document are given. Inhibitors designed to make more extended interactions with thrombin are also presented. II. Structure of Thrombin Page 248 Thrombin consists of two polypeptides, an A chain of 36 residues and a 259-residue B chain, linked by a disulfide bond. The crystallographic structure of thrombin reveals a globular protein organized about two β barrels with the overall folding pattern of the chymotrypsin serine protease family [6,7]. The catalytic triad and nearby oxyanion hole are located roughly between the β barrels and adopt the geometric arrangement required for serine-protease-assisted, peptide bond cleavage (Figure 1). Thrombin's multifunctionality and regulation of activity are achieved by specialized subsites on the enzyme's surface (Figure 2). Fibrinogen cleavage, for example, involves interactions at the primary specificity pocket, the extended fibrinogen recognition exosite, and an additional specificity pocket. Subsite interactions differ for cleavage of other thrombin substrates including the thrombin receptor and protein C. Additional and overlapping subsites exist for thrombin effector molecules including heparin, antithrombin III, and heparin cofactor II [8,9]. Figure 1 Stereoscopic view of the crystallographic structure of thrombin complexed with N-acetyl-(D-Phe)-Pro-boroArg-OH. Helical regions are represented in the standard way and arrows indicate regions of β sheet. Solid lines show the thrombin bound conformation of N-acetyl-(D-Phe)-Pro-boroArg-OH (taken from Reference 10). Active-site residues, His57 and Ser195, are shown with a ball-and-stick representation. The authors thank Dr. C. L. Strickland for the drawing. http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_248.html [4/5/2004 5:10:15 PM]
Document Figure 2 Schematic representation of Subsite Utilization in Thrombin Complexes (after Reference 8). Fibrinogen interacts with three thrombin subsites (here thrombin is represented by a large oval and the interconnected subsites by an irregular three-armed shape). Physiological effectors of thrombin and thrombin inhibitors form distinct interactions at these subsites. Additional subsites, such as the heparin-binding site, exist on the thrombin surface and are not indicated here. The catalytic triad is represented by three circles at the vertices of a triangle. http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_249.html (1 of 2) [4/5/2004 5:10:27 PM] Page 249
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Structure-based Drug Design 14 Stru
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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 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 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 reverse transcriptase inhi
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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 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 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 Figure 1 Reactions catalyz
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Document Figure 2 Structure of lico
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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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Page 257 and 258: Document 29. Baker ME. Genealogy of
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Page 263 and 264: Document Page 214 viruses. Specific
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Page 267 and 268: Document Page 218 The catalytic loo
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Page 271 and 272: Document Figure 3 (a) Ternary compl
Page 273 and 274: Document Figure 5 (a) Staurosporine
Page 275 and 276: Document protein kinase core is ess
Page 277 and 278: Document 10. Knighton DR, Zheng J-H
Page 279 and 280: Document 24. Madhusudan Xuong N-H,
Page 281 and 282: Document 9 Structural Studies of Al
Page 283 and 284: Document diverse ARIs have been sho
Page 285 and 286: Document Figure 3 C α trace of the
Page 287 and 288: Document Figure 4 Surface represent
Page 289 and 290: Document Figure 5 Schematic represe
Page 291 and 292: Document Figure 7 Stereo of zopolre
Page 293 and 294: Document B. Structures Figure 8 Seq
Page 295 and 296: Document This method was used to sc
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Page 301 and 302: Document 35. Pailhoux EA, Martinez
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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
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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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 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 323 been suggested th
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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 17. Szelke M. Chemistry of
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Document 34. Rosenberg SH, Plattner
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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 Figure 10 Structures of so
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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 Figure 12 Predicted bindin
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Document Page 388 nosine proved to
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Document 30. Kim H, Feil I, Verlind
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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 7 (a) Superposition
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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 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 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 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 Page 518 The differences b
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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 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 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 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 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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