Search pruning

These properties lead to pruning of the search tree. Branching then continues in the tree until the upper and lower bounds converge. 

The area of ruthenium and osmium coordination chemistry is vast and I am grateful to Professor Edwin Constable for carrying out the initial search of the literature and generating a database of over 12,000 references from which to start the pruning process. 

Several metasearch programs automate the process of submitting a query to multiple search engines. These include Metacrawler at http //www. metacrawler.com and SurfWax at http //www.surfwax.com./ Note that metasearch engines tend to have two drawbacks They may overwhelm you with results (and insufficiently prune duplicates), and they often do not use some of the more popular search engines (such as Google or Northern Light). 

Objective Find common feature configurations amongst a set of active molecules. Algorithm HipHop uses a pruned exhaustive search method. Starting with simple two-feature pharmacophores, the program tries to add one extra common feature at a time until no larger common pharmacophore configuration exists [10]. Combinations that cannot be completed to reach a minimum number of features are not further explored. 

Gehlen, J.N., Daizadeh I., Stuchebrukov, A. A., and Marcus, R. A. (1996) Tunneling matrix element in Ru-modified blue copper proteins pruning the protein in search of electron pathway, Inorg. Chim. Acta 243, 271-282. 

Figure 11. The combiBUILD algorithm (a) Starting point is a scaffold modeled into its target receptor. CombiBUILD goes over a database of possible reactants to add to the scaffold (b) CombiBUILD performs a systematic rotational search on each reactant (typically in 10-15 increments within the low energy minima for each torsion type), pruning for intramolecular clashes and bumps to make the search more efficient (c) CombiBUILD performs a rigid body minimization on each possible component conformation, scores it with a force-field scheme.

Case 2 The premises are the same as in case 1, but here we allow the formation of molecules with up to five functional groups. The total number of potential molecules is 1,712,304. The search algorithm has generated 4131 metamolecules and rejected 2,094 of them (Table XI). See footnotes of Table XI for constraints guiding the pruning of infeasible metamolecules. 

In the interest of pruning the search tree, we can use what is known about the sources and sinks to limit the alternatives to the more reasonable choices. 

Reduction of search space for matching (early pruning of dissimilar element pairs, partition-based matching)... 

Bioinformatics approaches to protein structure prediction and the identification of homology and similarities involve the solution of search problems. As the range of possible protein sequences and folding conformations is astronomical, appropriate pruning of the search space is inherently necessary. The so-called Levinthal paradox [4] states that even real proteins cannot try out all the possible conformations during the time they fold into... 

T o enhance the performance of grid searches, two advantages of the tree representation can be utilized. Firstly, parts of the tree that correspond to conformations with atom clashes or close contacts can be detected and pruned. Fig. 18 illustrates this for a conformation of n-heptane. Neither changes to the torsion xn nor to rn, will avoid the steric clash exhibited at the marked atoms. Thus, the search tree can be pruned above the node of xn i-... 

The performance of the original backtracking algorithm can be further improved by pruning-off fruitless branches of a search tree as early as possible. One technique for achieving this was introduced into a backtracking match algorithm by Ullmann in 1976 [16]. 

The combination of the new methods for optimizing and pruning search trees described above, and the backtracking technique, makes the Chen-Robien algorithm a very fast MCSS algorithm. It has become a central mainstay of several other commands within the CSEARCH-NMR database system [69]. 

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