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Document minimization phase, a more realistic distribution of functional group minima is generated. C. Thrombin Functionality Maps Page 547 Human thrombin is one of the best characterized enzymes from a structural point of view (Figure 3). It binds a series of diverse inhibitors without major rearrangements in its conformation, as shown by a number of x-ray crystallography studies [26,36–39]. Its S3 and S2 precleavage subpockets have hydrophobic character, whereas at the bottom of the S1 or recognition pocket the carboxy group of Asp189 is a salt bridge partner for basic side chains (Figure 3). D-phenylalanyl-L-prolyl-L-arginine chloromethane, PPACK, (Figure 4a), and Nα-((2-naphthylsulfonyl)glycyl)-DL-pamidinophenylalanylpiperidine, NAPAP, (Figure 4b) are the archetypal active-site inhibitors of thrombin. The crystal structure of the thrombin-NAPAP complex is shown in Figure 3. The PPACK and NAPAP inhibitors bind to the thrombin active site by occupying the S3 and S2 pockets with their hydrophobic moieties and by positioning their basic group (guanidinium of PPACK, benzamidine of NAPAP) into S1 to form a salt bridge with Asp189. In continuation of a project aiming at the structure-based design of low molecular weight, active-site directed inhibitors of human thrombin [40], MCSS was used to generate a series of functionality maps of the thrombin S3 to S2' pockets [20,28]. A detailed description of the thrombin functionality maps and the continuum approximation used to postprocess the MCSS minima is given in Reference [28]. From the analysis of the results for the nonpolar groups it is evident that hydrophobic moieties prefer to bind to the S3 and S2 pockets (Figure 5). The solvent exposed face of the Trp60D indole is another favorable site, though the intermolecular van der Waals interactions are much smaller. Binding to the S2' region is favored by interactions with the Leu40 side chain but implies a desolvation penalty because of the burial of part of the Arg73 guanidinium and/or the Gln151 side chain. The latter might be an artifact of the rigid protein structure used in the minimization, since the side chains of Arg73 and Gln151 are flexible enough to displace their polar groups towards a more exposed region. Binding to the neighboring Leu41 side chain in S1' is highly unfavorable because of the concomitant desolvation of Lys60F. For polar groups with zero net charge there are several hydrophylic groups on the thrombin main chain that might be involved in strong hydrogen http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_547.html [4/9/2004 12:51:56 AM]
Document Figure 3 (a) Stereo view of the thrombin molecule in its complex with NAPAP. The side chains of thrombin involved in the binding of NAPAP and the disulfide bridges are shown in stick-and-ball representation with black sticks. NAPAP is shown in stick-and-ball representation with white sticks. (b) Zoom image of the active site region. Figures made with the program MOLSCRIPT [42]. Page 548 bonds. These are 214CO, 216NH, 216CO, and 219NH in S1; 193NH and 195NH in the oxyanion hole; 41CO in S1'; 40CO in S2'; and 147NH and 148NH on the autolysis loop, whose exposure is dependent on crystallization conditions and inhibitor type. Two main conclusions can be drawn from the analysis of the minimized positions of the charged functional groups. First, the minima with the lowest binding free energy have optimal hydrogen bonds with the Asp189 side chain in the S1 pocket. Representative examples are the lowest energy minimum of benzamidine (Figure 5) and the lowest energy minima of methylguanidinium and methylammonium (Figure 4 of Reference 28). Since the Asp189 side chain http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_548.html (1 of 2) [4/9/2004 12:52:27 AM]
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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 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 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 Bradykinin Receptor Anta
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Document Page 121 Nearly all cells
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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 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 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 20. Murphy G, Docherty AJP
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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 Page 218 The catalytic loo
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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 Cyclotheonamide A (CtA), a
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Document balance its pro- and antic
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Document Figure 1 The coagulation c
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Document Table 2 Naturally Occurrin
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Document Table 3 Active Site Sequen
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Document Lys in the P1 position is
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Document 12 Polypeptide Modulators
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Document A. Chemical Modification P
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Document Page 314 anemone toxins an
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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 17. Szelke M. Chemistry of
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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 7 (a) Superposition
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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 5. Dinarello CA. On the Bi
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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 Page 462 strains of influe
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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 VI. Conclusion Page 480 It
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Document 21. Both GW, Sleigh MJ, Co
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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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Page 639 and 640: Document conformational transition
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Page 673 and 674: Document 21 Structure-Based Combina
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Page 685 and 686: Document Lists of Bonding Fragment
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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
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Page 697 and 698: Document 22 Peptidomimetic and Nonp
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Document Acknowledgments Page 620 I
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Document 18. Sawyer TK. In: Peptide
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Document MA, Welch KM, Hallak H, Ta
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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 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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