The Search Algorithm

To overcome the limitations of the database search methods, conformational search methods were developed [95,96,109]. There are many such methods, exploiting different protein representations, objective function tenns, and optimization or enumeration algorithms. The search algorithms include the minimum perturbation method [97], molecular dynamics simulations [92,110,111], genetic algorithms [112], Monte Carlo and simulated annealing [113,114], multiple copy simultaneous search [115-117], self-consistent field optimization [118], and an enumeration based on the graph theory [119]. 

The major difficulty that the search algorithm has to face for long chains is that it is hardly possible to make any changes in the torsion angles without creating significant overlaps of atom pairs. Successful attempts to move sev-... 

The search algorithm employs a successive approximation and accelerated convergence technique on the Independent variable in eqn (6), then approximates the dependent variable from the simultaneous solution of the equations for Mn and Mw moments of the polydisperse standard distribution. Convergence to within 0.1% of true and values of a broad MWD standard is usually achieved in six to nine iterations. 

The purpose of this study was to evaluate the linear calibration technique employing a single polydisperse standard and the search algorithm described above for non-aqueous and aqueous SEC. Comparison of this calibration technique to peak position, universal calibration, and Q-factor approximation techniques which make use of a series of narrow MWD polystyrene standards was also carried out. 

Dextran polymers were used to evaluate the utility of the linear, polydisperse calibration method for water-soluble polymer characterization. A blend of T-40 and T-70 dextran standards was used as a polydisperse calibration standard. Table VIII displays the report from the linear calibration method using this standard. Nine Iterations of the search algorithm were required for convergence to the true and Mn values of the standard. As can be seen in the report, the elution volume profile of the standard contained 72 area/time slices upon which calibration calculations were based. The slice width was set at 10 seconds/siIce. Figure 5 shows a plot of the calibration curve generated from the linear calibration method utilizing the dextran standard,... 

The search algorithm required 26 iterations or trials to reach the optimum formula. Below the formulation, there appears the profile of expected attribute ratings corresponding to that formulation. 

It would normally require more than 25 samples in a learning set to produce a really good equation. Despite this less than optimum number, the search algorithm was able to identify a combination of five wavelengths (from the 19 discrete filters in the InfraAlyzer 400 system) and generate an equation which could extract carbohydrate and water concentrations from spectra which came from highly colored material. Clearly, the NIRA technique shows promise for this analysis. 

Raman, and nmr spectra. An extensive bibliography of older hard-copy ir spectra is given in The Coblent Sodety Desk Book of Infrared Spectra (62). Since the mid-1980s, comprehensive databases have been available in computerized form where the spectra themselves, not merely the bibliographic references, are searchable and displayable. The search algorithms vary considerably among the available systems no algorithm standard exists (ca 1994), but several are under development (63,64). Expert systems, which assist in the automatic interpretation and identification of spectra, have existed for many years but are not commonly used (65). Computerized spectral databases are either local, PC-based, or public. 

When the penalty multiplier is large, constraint violations are discouraged and the search algorithm is biased toward satisfying constraints at the expense of minimizing pumping. 

Fig. 4.15 Hit list from Feature Tree fragment space searches are grouped by a molecular framework analysis (y-axis) and the Feature Tree similarity score (x-axis). The search algorithm indeed produces compounds from...

In summary, pharmacophore model validation is the building of a body of evidence by first relying on validation methods adapted to the search algorithm (and its limitations) and second by resorting to approaches that will incorporate external data and therefore account for some inherent imperfections of the dataset. The first section of this chapter will report some of the most used validation methods and which are related to one or both of these aspects. 

Once the physical topology of the self-assembly is formed in the NanoCell, it remains static there is no molecule or nanoparticle dynamic character (other than bond rotations or vibrations) to the highly crosslinked network. The only changeable behavior is in the molecular states conducting ON or non-conducting OFF, as set by voltage pulses from the periphery of the cell, or as defined by the search algorithms in these simulations. 

Since its first introduction in 1982, the DOCK software has been extended in several directions. The matching spheres can be labeled with chemical properties,61 and distance bins are used to speed up the search process.62,63 Recently, the search algorithm for distance-compatible matches was changed28 to the clique-detection algorithm introduced by Crippen and co-workers.55 Furthermore, several scoring functions are now applied in combination with the DOCK algorithm.64-68... 

The parameters to be optimized for experimental recombination include the crossover frequency, the number of parents, and the sequence similarity between parents. Additionally, it is important to understand the conditions under which recombination is useful. For all these questions, the optimal parameters represent a balance between the exploration and exploitation capabilities of the search algorithm. Any process that creates more diversity, such as using many parents, very disparate parents, or small fragment sizes, will improve exploration at the cost of exploitation. The balance between these effects will shift according to the landscape ruggedness and the sampling ability of the mutant library. 

Searching the spectrum of an unknown chemical against a spectral library is a routine method used to identify chemicals. Most of the commercial infrared instruments include library search software that has several search algorithms to choose from. The search algorithm can sometimes have a strong effect on the library search result. This is due to the different ways the actual comparison between the spectra is done. Especially when the library and the unknown spectra have been measured differently (e.g. using solid KBr disk and cryodeposition GC/FTIR), the... 

Figure 6. An example of a library search. An unknown chemical was searched against a library containing chemicals related to the CWC. The first hit, dimethyl ethylphosphonate was clearly the best candidate and matches the unknown. The search algorithm was a square derivative and the maximum HQI value is 999. (Source M. Sbderstrom, unpubhshed...

Also shown in Exhibit 31.3 is a web-based e-transaction where both FRl and FR2 are influenced by DPI, but only FR2 is influenced by DP2. In other words, the home page design (DPI) determines what shows on the home page (FRl) and enables further searching (FR2) but the search algorithm (DP2) does not determine what is showing on the home page (FRl), and only enables the identification of additional products for sale (FR2). 

Thus the search algorithm for the canonical incidence matrix of a hypergraph includes the following steps ... 

This subsection discusses the search algorithms to treat ligand flexibility and to some extent protein flexibility. A representative set of the currently reviewed docking programs is summarized in Table 6. 

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