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Document Table 5 Crystallographic Cocktail Soaking Experiments of Trypanosomal TIM Crystals a res DTT X C a(Å) b(Å) c(Å) m(°) (Å) R-sym Compl R (σ) (σ) 1 112.7(1) 97.7(1) 46.7(1) 0.7 2.85 0.044 0.97 0.136 5.0 3.5 1A 112.6(1) 97.6(1) 46.8(1) 0.9 2.50 0.099 0.96 0.173 7.0 2.0 1B 112.7(2) 97.5(3) 46.8(2) 0.7 2.30 0.044 0.88 0.172 5.0 4.0 1BA 112.6(2) 97.9(2) 46.7(2) 0.7 2.40 0.051 0.96 0.202 7.8 3.0 1BB 112.6(1) 97.8(1) 46.7(1) 0.7 2.30 0.034 0.90 0.203 5.0 3.0 2 112.9(1) 97.8(1) 46.7(1) 0.9 2.40 0.060 0.92 0.172 5.0 - 3 112.9(1) 97.7(3) 46.7(2) 0.7 2.40 0.057 0.93 0.170 4.0 - a The following data are tabulated column-wise: C = cocktail; a, b, c = cell parameters of the P212 12 1 crystals; m = mosaicity; res = resolution; R-sym = agreement between symmetry-related reflections; Compl = completeness; R = agreement between data and model; DTT = signal of oxidized DTT in the final difference Fourier map. DTT is present in the mother liquor but not incorporated in the model. X = signal of peak X in the final difference Fourier map. Maps were calculated with data between 10.0 Å and the high resolution limit. trostatic scoring, where the linearized Poisson-Boltzmann equation is solved [78]. We report here on docking experiments to identify GAPDH inhibitors from the Available Chemicals Directory-3D 93 (ACD) [80]. Force-field scoring and electrostatic scoring require the assignment of partial atomic charges. Unfortunately, such charges are not available in the ACD, mainly because there is no consensus on a method to calculate them. Since the number of molecules in the ACD is very large, about 73,000 in 1993, we opted for the charge-equilibration algorithm developed <strong>by</strong> Rappé and Goddard [81] as implemented in the BIOGRAF program [82]. This method leads to charges that are in excellent agreement with experimental dipole moments and with atomic charges obtained from electrostatic potentials of accurate ab initio calculations. A script was written that processed the entire ACD automatically on an R4000 processor in about two days. Charges of the protein atoms were assigned from the table of AMBER-derived charges provided with DOCK 3.5. http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_381.html (1 of 2) [4/5/2004 5:40:43 PM] Page 381
Document Because there are tens of parameters that can be varied in the program there is no such a thing as the DOCK run for a given protein target. We chose to perform two parallel runs that differ in receptor description. In run 1 the DOCK sphere center description was used while in run 2 the atomic coordinates of 2'- deoxy-2'-(3-methoxybenzamido)adenosine, a designed selective inhibitor of T. brucei GAPDH (see Section IV), were picked to describe the receptor site. For each run the same program parameters were chosen (Table 6) and the ACD database was split up in batches of 10,000 molecules. The computation was done on an Indigo2 workstation with an R4400 processor operating at 175 MHz. It took 3 h 19 min of CPU time for run 1 and 34 h 48 min for run 2. The ten-fold time difference between the two runs originates from the different number of http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_381.html (2 of 2) [4/5/2004 5:40:43 PM]
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Document D ddI, 152 tumour necrosis
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Document antistasin peptides, 281 c
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Document [Protease targets] serinyl
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