A Geometric Buildup Algorithm for the Molecular Distance Geometry Problem

摘要: A. 1 MDGP sizes for benchmark structures at different cutoffs........ 31 A. 2 Results of geometric buildup with clusters algorithm described in Figure 5.2 parameterized by different number of generations applied to the benchmark set of protein structures. The value of the distance cutoff used to generate the problem instance is 5Å. The instances where the algorithm was able to determine the coordinates of all atoms with the RMSD less than 0.01 are indicated in green, ie, the problem is solved. 32 A. 3 Results of geometric buildup with the clusters algorithm described in Figure 5.2 parameterized by different number of generations applied to the benchmark set of protein structures. The value of the distance cutoff used to generate the problem instance is 6Å. The instances where the algorithm was able to determine the coordinates of all atoms with the RMSD less than 0.01 are indicated in green, ie, the problem is solved. 33 A. 4 Results of geometric buildup with the clusters algorithm described in Figure 5.2 parameterized by different number of generations applied to the benchmark set of protein structures. The value of the distance cutoff used to generate the problem instance is 7Å. The instances where the algorithm was able to determine the coordinates of all atoms with the RMSD less than 0.01 are indicated in green, ie the problem is solved. 34