Search/Compare

Because licensed vaccines are the focus of much attention in the public as well as in the vaccine research community, VIOLIN has two subdatabases that focus on licensed human and animal vaccines. The Huvax subdatabase (http //www.violinet.org/huvax) stores all licensed human vaccines in the USA and Canada. The data for these licensed human vaccines are annotated through manual curation and a vigorous review process. Huvax includes manually curated data including manufacturer, trade name, storage information, age at which the vaccine should be administered, and other relevant information. These vaccines are also listed by the CDC CVX codes (codes that indicate the product used in a vaccine) for tracking vaccination records. Huvax has provided cross-references based on these CDC CVX codes. Huvax provides ways for users to search, compare, and analyze licensed human vaccines. Various criteria can be used for querying human vaccines. Different vaccines can also be compared side by side. Vevax is a VIOLIN database of licensed veterinary vaccines (http //www. violinet.org/vevax). 

Borkent, J.H., Oukes, F., and Noordik, J.H. 1988. Chemical reaction searching compared in REACCS, SYNLIB and ORAC. Journal of Chemical Information and Computer Science, 28(3) 148-150. 

Two types of library search have been developed. The first type, called forward search, compares the new spectrum with the spectra stored in the library and looks for the best match of the spectra. The second type, called reverse search, checks for the possible presence in the new spectra of a spectrum chosen in the library. 

Figure 7. a) Typical flight behaviour of a male moth tracking a pheromone plume released by a female moth, b) Trace of a typical pheromone search compared to the structure of the pheromone plume. (Image on top by Ishida Morizumi 2002 [40] bottom image by J.Hildebrand). 

Similarity search was developed as an effort to remove the limitations of substruc-tnre search [72]. A similarity search compares a set of characteristics describing the target structure with the corresponding structure with the set of characteristics of... 

Pig. 2. This figure shows the result of performing a TBLASTN search against the nonre-dundant (NR) GenBank database using the peptide sequence of the tomato ZDS minus the transit peptide sequence (17). A TBLASTN search compares the amino acid input to the translated nucleotide sequences contained in the database (55,56). Presented by the permission of NCBI. 

M-Base Engineering + Software GmbH in Aachen, Germany (www.m-base.de) makes available a program, MCBase, that allows the user to search, compare, and perform queries of all CAMPUS data that the user has loaded into the databank. MCBase has several features not available in CAMPUS such as WEE and power-law curve fitting of viscosity data, substitute grade search, exclude function, and enhanced text search options. 

The first three searches compared the performance of different similarity measures with the full INBS frequency data. When the performance of the frequency Tanimoto measure and the city block metric was compared, it was found that the hits ranked to the top using the Tanimoto measure were not as similar to the query structure as those ranked top by the city block metric. Generally it was found that the city block and Euchdean distance measures ranked the hits equally well, however in two cases the city block ranking was better than the Euclidean ranking, so use of the city block metric may be preferred. The fourth search used only the paths from the most connected atom in the structure in a city block metric calculation. A comparison of the performance of the INBS search for individual query structures using the city block metric for all paths and for the Morgan root atom alone is discussed below. 

To search for the forms of potentials we are considering here simple mechanical models. Two of them, namely cluster support algorithm (CSA) and plane support algorithm (PSA), were described in details in [6]. Providing the experiments with simulated and experimental data, it was shown that the iteration procedure yields the sweeping of the structures which are not volumetric-like or surface-like, correspondingly. While the number of required projections for the reconstruction is reduced by 10 -100 times, the quality of reconstruction estimated quantitatively remained quite comparative (sometimes even with less artefacts) with that result obtained by classic Computer Tomography (CT). 

First, a quei y must be drawn using the MOL" ISIS/Draw program. By using this reaction query, a eurrent reaction search " can be performed. This type of reaction retrieval compares the starting material and the product of the reaction query with all the reactions in the CIRX database. Both query structures must match exactly, including the implicit hydrogen atoms not shown in the reaction query. In this case, one hit is found in the CIRX databases. 

In order to perform a database search the structural key of the query molecule or substructure is compared with the stored structural keys of the database entries. This implies that each array element in the structural key has to be defined initi-... 

After an alignment of a set of molecules known to bind to the same receptor a comparative molecular field analysis CoMFA) makes it possible to determine and visuahze molecular interaction regions involved in hgand-receptor binding [51]. Further on, statistical methods such as partial least squares regression PLS) are applied to search for a correlation between CoMFA descriptors and biological activity. The CoMFA descriptors have been one of the most widely used set of descriptors. However, their apex has been reached. 

The advan tage ol a conjugate gradien t m iniim/er is that it uses th e minim i/ation history to calculate the search direction, and converges t asLer Lhan the steepest descent technique. It also contains a scaling factor, b, for determining step si/e. This makes the step si/es optimal when compared to the steepest descent lechniciue. 

Dmparison of various methods for searching conformational space has been performed cycloheptadecane (C17H34) [Saunders et al. 1990]. The methods compared were the ematic search, random search (both Cartesian and torsional), distance geometry and ecular dynamics. The number of unique minimum energy conformations found with 1 method within 3 kcal/mol of the global minimum after 30 days of computer processing e determined (the study was performed in 1990 on what would now be considered a / slow computer). The results are shown in Table 9.1. 

D database searching. As each conformation is generated an appropriate bit is set in the binary key. At me, the binary key appropriate to the pharmacophore is set up and compared with the keys in the database. 

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