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Document Table 6 Parameters Chosen for the DOCK Runs with T. brucei GAPDH a Program Variable Value Program Variable Value SPHGEN dentag X DOCK distance_tolerance 1.0 dotlim 0.0 nodes_maximum 4 radmax 5.0 nodes_minimum 4 radmin 1.0 ligand_binsize 0.4 DISTMAP polcon 2.3 ligand_overlap 0.1 ccon 2.8 receptor_binsize 0.8 discut 4.5 receptor_overlap 0.2 perang 3 atom_minimum 5 a Variables as defined in the DOCK 3.5 manual and discussed in References 79 and 83. centers to describe the receptor, namely 20 for run 1 and 34 for run 2. According to theory [83], the difference should scale as 34 4/20 4 = 8.3, which fits our observation. Since it is well known that scores exhibit poor correlation with real affinities [84] we decided to subject the 200 best-scoring ligands of each batch to inspection on the graphics. Scanning through the 3200 compounds required about ten days. Eventually, sixteen compounds were selected for purchase on Table 7 Parasite GAPDH Inhibitors Discovered with DOCK Contact Delphi Inhibitor IC 50 (mM) Score Rank Score Rank Run 1 2-Guanidinobezimidazole 1.2 97 1432 1.01 1427 2-Benzimidazoylurea 1.8 102 958 0.27 1241 4-Nitrophenyl sulfone 2.8 106 608 -0.46 370 Tryptophan 6.0 128 32 -0.48 357 http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_382.html (1 of 2) [4/5/2004 5:40:52 PM] Page 382
Document 5-Methoxytryptamine 19.0 92 1495 -0.32 488 Ephedrine 25.0 99 1315 -0.22 590 Epinephrine >7 a 102 989 -3.09 27 Aspartic acid dimethyl ester >10 87 1551 -1.66 146 3-Amino-L-tyrosine >11 a 102 969 -0.14 703 1,3-Diphenylguanidine >11 a 112 301 -1.28 209 Octopamine >50 a 106 660 -2.03 83 Run 2 2-Nitrobenzoic acid hydrazide 4.4 132 900 0.11 1112 Dopamine 12.0 143 241 -2.02 156 Norepinephrine >5.4 a 151 84 -2.09 137 4'-Amino-N-methyl acetanilide >7.8 a 131 1027 0.04 1021 L-histidinol >9.3 142 300 0.13 1156 a Could not be tested at higher concentrations due to solubility problems. http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_382.html (2 of 2) [4/5/2004 5:40:52 PM]
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netLibrary - eBook Summary Universi
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Structure-based Drug Design 14 Stru
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Document 2 Structural Studies of HI
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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 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 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 163. Lacey SF, Larder BA.
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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 123 were poorly satis
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Document receptor, it has not yet b
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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 We determined the structur
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Document IV. Drug Design Progressio
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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 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 Page 441 sequence of the m
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Document Page 476 nM, respectively.
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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 Acknowledgments Page 620 I
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Document 18. Sawyer TK. In: Peptide
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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 Kininogen, 119 high molecu
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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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