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Document Figure 6 Schematic representation of the CCLD program. Variable assignments are symbolized by :=. Conditional statements are enclosed by diamonds. [From Reference 28.] http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_551.html (1 of 2) [4/9/2004 12:53:13 AM] Page 551
Document Lists of Bonding Fragment Pairs and Overlapping Fragment Pairs Page 552 The user has to specify for each functional group type which atoms are to be used for connection to other fragments. For each linkage atom CCLD generates a set of possible linkage points, i.e., points that will be used to determine the position and orientation of the link. All possible pairs of minimized positions are then analyzed and added to the list of bonding fragment pairs if they can be linked; otherwise, if two fragments have bad contacts they are added to the list of overlapping fragment pairs. A pair of bonding fragments may be connected by a linker unit, by a single covalent bond (1-bond), or by fusing two overlapping atoms belonging to different fragments (0-bond). The linker units are small since their function is to optimally connect two fragments without adding considerably to the molecular weight. The following linker elements have been implemented so far: Keto and methylene (2-bond), amide and ethylene (3-bond). The user is free to choose minimal and maximal values for the distance (d) between linkage atoms for each connection type. In the application to thrombin the following values in Ångstroms were used: d
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Structure-based Drug Design 14 Stru
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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 15 Thiazoles are less
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Document Figure 5 Stereo view AG134
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Document Page 23 potentially loweri
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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 36. Leytus SP, Chung DW, K
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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 314 anemone toxins an
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Document 13 Rational Design of Reni
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Document Page 323 been suggested th
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Document Page 327 this analog inter
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Document 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 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 II. Three Glycolytic Enzym
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Document Figure 6 Stereoview of NAD
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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 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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Page 637 and 638: Document Page 514 sis. Large number
Page 639 and 640: Document conformational transition
Page 641 and 642: Document Page 518 The differences b
Page 643 and 644: Document 10. Mast EE, Harmon MW, Gr
Page 645 and 646: Document 25. Arnold E, Rossmann MG.
Page 647 and 648: Document 44. Argos P, Rossmann MG,
Page 649 and 650: Document 63. Rozhon E, Cox S, Buont
Page 651 and 652: Document 81. Diana GD, McKinlay MA,
Page 653 and 654: Document 20 The Integration of Stru
Page 655 and 656: Document Page 527 function. Iterati
Page 657 and 658: Document Figure 3 Generation of com
Page 659 and 660: Document Page 530 screen. For examp
Page 661 and 662: Document ciency of drug discovery (
Page 663 and 664: Document Page 533 the reactions are
Page 665 and 666: Document Page 535 by factoring in a
Page 667 and 668: Document Page 537 ries, holds the p
Page 669 and 670: Document 17. Zuckermann RN, Martin
Page 671 and 672: Document 34. Fei Y-J, Kanai Y, Nuss
Page 673 and 674: Document 21 Structure-Based Combina
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Page 677 and 678: Document Page 545 protein binding s
Page 679 and 680: Document Figure 2 Stereo view of th
Page 681 and 682: Document Figure 3 (a) Stereo view o
Page 683: Document Figure 5 Stereo view of th
Page 687 and 688: Document Figure 8 Minimized structu
Page 689 and 690: Document Page 555 N-acylpyrrolidine
Page 691 and 692: Document 10. Bobbyer DNA, Goodford
Page 693 and 694: Document structure. 2. Ligand probe
Page 695 and 696: Document 30. O'Shea EK, Rutkowski R
Page 697 and 698: Document 22 Peptidomimetic and Nonp
Page 699 and 700: Document Figure 1 Examples of nativ
Page 701 and 702: Document B. Peptidomimetic Drugs: C
Page 703 and 704: Document Figure 4 Backbone amide bo
Page 705 and 706: Document 12640-0567a.gif Figure 6 C
Page 707 and 708: Document Page 569 molecule. A nonco
Page 709 and 710: Document cases, a pharmacophore mod
Page 711 and 712: Document Figure 9 Peptide scaffold-
Page 713 and 714: Document Figure 11 Protease-targete
Page 715 and 716: Document Figure 12 Peptide scaffold
Page 719 and 720: Document Figure 14 Signal-transduct
Page 725 and 726: Document Figure 17 Nonpeptide drug
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Document Page 595 the MC1 receptor
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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
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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 Page 623 53. Bird J, Harpe
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Document 78. Rodriguez M, Crosby R,
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Document MA, Welch KM, Hallak H, Ta
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Document Page 626 SJ, Ogden RC, Red
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Document 97; (e) Fujii I, Nakamura
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Document Med Biol 1991; 306:9-21; (
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Document Page 629 ML, Clare M, Decr
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Document Page 630 177. (a) Bode W,
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Document Page 631 197. Musil D, Zuc
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Document son AH, Drummond AH, Huxle
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Document 236. (a) Marshall MS. TIBS
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Document 274. (a) Kavanaugh WM, Wil
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Document replacements, 563-565 1-am
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Document inhibitor binding, 323, 33
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Document site, 52, 55, 61 triad, 24
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Document factors, 247 Combination t
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Document Cyclotheonamide A (CtA), 2
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Document D ddI, 152 tumour necrosis
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Document antistasin peptides, 281 c
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Document fragment-based programs, 5
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Document [Human immunodeficiency vi
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Document overview, 103-104, 108-109
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Document [Inhibitors] 2-((3,4-dihyd
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Document antagonistic activity, 416
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Document [Interleukin-1] homology w
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Document Kininogen, 119 high molecu
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Document Matrix-metalloproteinase (
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Document RT inhibitor, 41, 56 Nonpe
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Document Phosphoglycerate kinase (P
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Document [Protease targets] serinyl
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