Search algorithm evaluation

TJA Ewing, ID Kuntz. Critical evaluation of search algorithms for automated molecular docking and database screening. J Comput Chem 18 1175-1189, 1997. 

A typical line search algorithm, which uses the derivative of r(a) evaluated at a = 0, denoted by r (0), is... 

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 SEQUEST database search algorithm (Ch. 17.6.2) is a powerful tool in protein identification, although like any statistical tool it relies on the jndgments of the user to critically evaluate its results. Problems may especially arise, when unanticipated modifications are present in the protein investigated. 

Evaluation of the Search Algorithm Taming the Combinatorial Explosion... 

Analytic Evaluation of Nonadiabatic Coupling Terms and Efficient Searching Algorithm of Conical Intersections within the COLUMBUS Program System Szalay V. 

Ewing, T. J. A. Kuntz, I. D., Critical evaluation of search algorithms used in automated molecular docking,./. Comput. Chem. 1997,18, 1175-1189... 

There are many other methods that can be used to separate proteins before characterization by mass spectrometry. Often in characterizing unknown proteins in a mixture, the constituent polypeptides are first enzymatically digested to yield a mixture of peptides. The peptides then are analyzed by MS either with or without some prior chromatographic or electrophoretic separation. With the aid of database search algorithms, the MS data are then evaluated to identify the proteins represented in the mixture (Abersold and Mann, 2003 Elia et ah, 2005). 

Optimizing a univariate function is rarely seen in pharmacokinetics. Multivariate optimization is more the norm. For example, in pharmacokinetics one often wishes to identify many different rate constants and volume terms. One solution to a multivariate problem can be done either directly using direct search (Khora-sheh, Ahmadi, and Gerayeli, 1999) or random search algorithms (Schrack and Borowski, 1972), both of which are basically brute force algorithms that repeatedly evaluate the function at selected values under the... 

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