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Document 26. Hilpert K, Ackermann J, Banner DW, Gast A, Gubernator K, Hadvary P, Labler L, Müller K, Schmid G, Tschopp T, van de Waterbeemd H. Design and synthesis of potent and highly selective thrombin inhibitors. J Med Chem 1994; 37:3889–3901. 27. Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem 1983; 4:187–217. 28. Caflisch A. Computational combinatorial ligand design: Application to human α-thrombin. J Computer-Aided Molec Design 1996; 10:372–396. 29. Gelin BR, Karplus M. Sidechain torsional potentials and motion of amino acids in proteins: bovine pancreatic trypsin inhibitor. Proc Natl Acad Sci USA 1975; 72:2002–2006. http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_557.html (2 of 2) [4/9/2004 12:53:41 AM]
Document 30. O'Shea EK, Rutkowski R, Kim PS. Evidence that the leucine zipper is a coiled coil. Science 1989; 243:538–542. 31. O'Shea EK, Klemm JD, Kim PS, Alber T. X-ray structure of the GCN4 leucine zipper, a twostranded, parallel coiled coil. Science 1991; 254:539–544. Page 558 32. Warwicker J, Watson HC. Calculation of the electric potential in the active site cleft due to α-helix dipoles. J Mol Biol 1982; 157:671–679. 33. Gilson MK, Honig BH. Calculation of the total electrostatic energy of a macromolecular system: solvation energies, binding energies, and conformational analysis. Proteins: Structure, Function, and Genetics 1988; 4:7–18. 34. Bashford D, Karplus M. pK as of ionizable groups in proteins: atomic detail from a continuum electrostatic model. Biochemistry 1990; 29:10219–10225. 35. Davis ME, Madura JD, Luty BA, McCammon JA. Electrostatics and diffusion of molecules in solution: simulations with the University of Houston Brownian dynamics program. Comp Phys Comm 1991; 62:187–197. 36. Bode W, Mayr I, Baumann U, Huber R, Stone SR, Hofsteenge J. The refined 1.9-Å crystal structure of human α-thrombin: interaction with D-Phe-Pro-Arg chloromethylketone and significance of the Tyr- Pro-Pro-Trp insertion segment. EMBO J 1989; 8:3467–3475. 37. Banner DW, Hadvary P. Crystallographic analysis at 3.0-Å resolution of the binding to human thrombin of four active site-directed inhibitors. J Biol Chem 1991; 266:20085–20093. 38. Obst U, Gramlich V, Diederich F, Weber L, Banner DW. Design neuartiger, nichtpeptidischer Thrombin-Inhibitoren und Struktur eines Thrombin-Inhibitor-Komplexes. Angew Chem 1995; 107:1874–1877. 39. Håkansson K, Tulinsky A, Abelman MM, Miller TA, Vlasuk GP, Bergum PW, Lim-Wilby MSL, Brunck TK. Crystallographic structure of a peptidyl keto acid inhibitor and human α-thrombin. Bioorganic and Medicinal Chemistry 1995; 3:1009–1017. 40. Tapparelli C, Metternich R, Ehrhardt C, Cook NS. Synthetic low-molecular weight thrombin inhibitors: molecular design and pharmacological profile. TIPS 1993; 14:366–376. 41. Holloway MK, Wai JM, Halgren TA, Fitzgerald PMD, Vacca JP, Dorsey BD, Levi RB, Thompson WJ, Chen LJ, deSolms SJ, Gaffin N, Ghosh AK, Giuliani EA, Graham SL, Guare JP, Hungate RW, Lyle TA, Sanders WM, Tucker TJ, Wiggins M, Wiscount CM, Woltersdorf OW, Young SD, Darke PL, Zugay JA. A priori prediction of activity for HIV-1 protease inhibitors employing energy minimization in the active site. J Med Chem 1995; 38:305–317. http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_558.html (1 of 2) [4/9/2004 12:53:43 AM]
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netLibrary - eBook Summary Universi
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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 monophosphate analogs whic
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Document Analysis of various HIV-1
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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 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 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 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 -62° for HIV-1 integrase,
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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 receptor, it has not yet b
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Document Page 137 observed for the
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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 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 IX. S2' Interactions 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 Cyclotheonamide A (CtA), a
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Document balance its pro- and antic
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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 All effects of the IL-1 fa
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Document Figure 13 The identified p
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Document 39. Saurat JH, Schfferli J
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Document receptor antagonist into a
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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 for directed subcellular t
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Document Page 462 strains of influe
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Document B. Protein Structure Page
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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 21. Both GW, Sleigh MJ, Co
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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 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 667 and 668: Document Page 537 ries, holds the p
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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
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Page 697 and 698: Document 22 Peptidomimetic and Nonp
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Page 707 and 708: Document Page 569 molecule. A nonco
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Page 735 and 736: Document Page 595 the MC1 receptor
Page 739 and 740: Document Figure 22 Protease 3D stru
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Document Figure 32 PTP and PTB 3D s
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Document Acknowledgments Page 620 I
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Document 18. Sawyer TK. In: Peptide
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Document Page 622 Fukuroda T, Fukam
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Document 78. Rodriguez M, Crosby R,
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Document MA, Welch KM, Hallak H, Ta
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Document 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 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 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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