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In the next case (Figure 3B), the GA run without crossover quickly found the structures between 6-8 ? RMSD, starting with 7.53 ? at the 308th generation. However, the GA with crossover found a better structure at the end around the 3000th generation. In the last example (Figure 3C), the GA with crossover identified a near native structure at a significantly earlier generation (136th) than without crossover, which yielded a near-native structure at the 2689th. Overall, the GA with crossover found a near-native structure at an earlier generation for two out of three cases. However, in one case (1ES7, Figure 3A) the actual computational cost for the GA with and without crossover was comparable. Impact of the population size and the clustering threshold Next, C59 wnt we tested four different population sizes (200, 400, 600, and 800) and three different pairwise clustering settings (10 ?, 5 ?, and not using the clustering step). Table 1 shows the summary of the best model (i.e. the model with the smallest RMSD) obtained by using GA runs for each setting. In addition to the RMSD of the best model, the rank of the fitness score, and the fnat, the fraction of native contacts [6], are also shown. Table 1 Summary of predictions using different population sizes and clustering thresholds ? ? No Pairwise Clusters 5? Pairwise Clusters find more https://www.selleckchem.com/products/epacadostat-incb024360.html 10? Pairwise Clusters PDB Population Size RMSD (?) 1 fnat 2 Rank RMSD (?) 1 fnat 2 Rank RMSD (?) 1 fnat 2 Rank 1ES7 200 17.51 0.03 20 17.94 0.03 16 1.86 0.92 3 ? 400 9.85 0.25 159 7.95 0.63 47 1.86 0.92 3 ? 600 14.21 0.00 445 9.56 0.34 265 1.86 0.92 3 ? 800 2.15 0.70 18 7.23 0.64 2 1.86 0.92 3 1K2X 200 18.52 0.00 84 21.20 0.01 61 6.05 0.49 74 ? 400 20.36 0.01 239 6.05 0.49 80 23.69 0.01 195 ? 600 6.14 0.46 250 2.12 0.51 1 23.41 0.01 599 ? 800 19.45 0.01 56 19.26 0.02 718 6.04 0.49 60 1WWW 200 19.16 0.02 51 13.49 0.11 152 8.62 0.58 23 ? 400 5.34 0.52 10 15.58 0.00 115 2.48 0.78 12 ? 600 17.37 0.03 248 15.76 0.03 182 11.12 0.39 13 ? 800 16.30 0.00 160 17.19 0.02 615 2.48 0.78 14 GA runs were carried out for 1000 generations. The crossover operation was not used. 1The Global C-�� RMSD between the best prediction in the final population and the native structure, for each simulation. 2fnat is the fraction of correctly predicted interface residues. The first observation is that results using the 10 ? cutoff showed the best RMSD models in ten out of twelve cases as compared with results without clustering and with the 5 ? cutoff. Comparing the no clustering and the 5 ? cutoff, the latter performed better than the former for seven out of twelve cases.