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Document [Catechol O-methyltransferase] drug complexes, 354-355 Mg++ ion, 349-350 S-adenosyl-L-methionine, 349 sequence, 345, 347 substrates, 345,346 Cation-p site, 277, 282 Ceriamide, 473 Charge calculation, 381 CHARMm, 133 databases, 536 selection algorithm, 536 systems integration, 536 virtual library production, 536 Chemotherapy, 66 Chimeric receptor, 126 Chymotrypsin serine protease family, 248 Coagulation cascade, 247, 265 Page 637 Chemical library, 142 Chemi-informatics, 526, 535, 537 Circular dichroism (CD), 438, 444 http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_637.html (1 of 4) [4/9/2004 1:52:52 AM]
Document factors, 247 Combination therapy, 62, 68, 69 approach, 550-552 chemistry, 141, 525, 537 combinatorial explosion, 552 drug lead source, 528, 529 focusing, 530 parallel synthesis, 528, 532 refinement, 530 robotic instrumentation, 528, 532 scaffolds, 530, 532 structure-activity relationship (SAR), 529 pruning, 552 Compound selection, 531 chemi-informatics, 536 drug properties, 535 receptor fit, 536 similarity, 536 structure-activity relationship (SAR) models, 533, 536 virtual libraries, 533, 536 Computer programs BIOGRAF, 381 http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_637.html (2 of 4) [4/9/2004 1:52:52 AM] Combinatorial
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netLibrary - eBook Summary Universi
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Structure-based Drug Design 14 Stru
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Document p17, p9, and p7) and repli
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Document Figure 1 Stereo view of th
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Document Figure 2 Schematic represe
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Document TF—transframe, PR—prot
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Document compounds that utilize sim
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Document Page 11 retroviral substra
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Document Page 13 of the active-site
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Document Page 15 Thiazoles are less
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Document Page 17 the resulting chim
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Document Figure 5 Stereo view AG134
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Document Page 23 potentially loweri
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Document Page 27 volume of the acti
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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 35. Kaldor SW, Hammond M,
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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 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 Figure 1 (Continued) this
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Document Page 218 The catalytic loo
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Document Page 220 conserved substra
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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 2. Lee AYW, Chung SK, Chun
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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 et al. [21]). Among these
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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 Figure 12 Modeled fit of S
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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 Page 291 21. Davie EW, Fuj
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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 Page 294 70. Seligmann B,
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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 5. Packer M, Gheorghiade M
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Document 42. Catterall WA, Beress L
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Document 60. Pennington MW, Zadenbe
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Document 76. Gould AR, Mabbutt BC,
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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 Figure 2 A schematic diagr
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Document Page 327 this analog inter
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Document Page 329 binding involves
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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 From quantitative structur
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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 Page 362 19. Lotta T, Vidg
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Document 35. Davis TL, Roznoski M,
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Document Figure 1 Available drugs f
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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 Page 376 was recently solv
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Document Because there are no known
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Document Page 379 For trypanosomal
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Document Because there are tens of
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Document 5-Methoxytryptamine 19.0 9
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Document Figure 11 Two-dimensional
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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 has a single membrane-span
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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 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 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 30. O'Shea EK, Rutkowski R
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Document Figure 4 Backbone amide bo
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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 Page 609 (e.g., thermolysi
Page 751 and 752: Document Figure 28 Protease 3D stru
Page 753 and 754: Document Figure 29 Protease 3D stru
Page 755 and 756: Document (Ser/Thr) peptide 2.9 Å 2
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Page 761 and 762: Document Page 617 Val (131) showed
Page 763 and 764: Document Figure 32 PTP and PTB 3D s
Page 765 and 766: Document Acknowledgments Page 620 I
Page 767 and 768: Document 18. Sawyer TK. In: Peptide
Page 769 and 770: Document Page 622 Fukuroda T, Fukam
Page 771 and 772: Document Page 623 53. Bird J, Harpe
Page 773 and 774: Document 78. Rodriguez M, Crosby R,
Page 775 and 776: Document MA, Welch KM, Hallak H, Ta
Page 777 and 778: Document Page 626 SJ, Ogden RC, Red
Page 779 and 780: Document 97; (e) Fujii I, Nakamura
Page 781 and 782: Document Med Biol 1991; 306:9-21; (
Page 783 and 784: Document Page 629 ML, Clare M, Decr
Page 785 and 786: Document Page 630 177. (a) Bode W,
Page 787 and 788: Document Page 631 197. Musil D, Zuc
Page 789 and 790: Document son AH, Drummond AH, Huxle
Page 791 and 792: Document 236. (a) Marshall MS. TIBS
Page 795 and 796: Document 274. (a) Kavanaugh WM, Wil
Page 797 and 798: Document replacements, 563-565 1-am
Page 799 and 800: Document inhibitor binding, 323, 33
Page 801: Document site, 52, 55, 61 triad, 24
Page 805 and 806: Document Cyclotheonamide A (CtA), 2
Page 807 and 808: Document D ddI, 152 tumour necrosis
Page 809 and 810: Document antistasin peptides, 281 c
Page 811 and 812: Document fragment-based programs, 5
Page 813 and 814: Document [Human immunodeficiency vi
Page 815 and 816: Document overview, 103-104, 108-109
Page 817 and 818: Document [Inhibitors] 2-((3,4-dihyd
Page 819 and 820: Document antagonistic activity, 416
Page 821 and 822: Document [Interleukin-1] homology w
Page 823 and 824: Document Kininogen, 119 high molecu
Page 825 and 826: Document Matrix-metalloproteinase (
Page 827 and 828: Document RT inhibitor, 41, 56 Nonpe
Page 829 and 830: Document Phosphoglycerate kinase (P
Page 831: Document [Protease targets] serinyl
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