Extended query

Extended query Select the databanks and click Extended button to open the extended query form. Enter query string to the Description field, name of the organism to the Organism field, and data string (yyyymmdd) in the Date field. Click Submit Query button to initiate the search. 

The CRC cannot obtain rapid answers to queries, often extending timelines for study closure. 

The refinement procedure utilises the fact that if some query node Q(X) has another node Q(fV) at some specific distance ) ( and/or angle), and if some database node D(Z) matches with Q(W), then there must also be some node D(Y) at the appropriate distance(s) from D(Z) which matches with Q(X) this is a necessary, but not sufficient, condition for a subgraph isomorphism to be present (except in the limiting case of all the query nodes having been matched, when the condition is both necessary and sufficient). The refinement procedure is called before each possible assignment of a database node to a query node and the matched substructure is increased by one node if, and only if, the condition holds for all nodes W, X, Y and Z. The basic algorithm terminates once a match has been detected or until a mismatch has been confirmed [70] it is easy to extend the algorithm to enable the detection of all matches between a query pattern and a database structure, as is required for applications such as those discussed here. 

Ill, or IV) can be initiated by selecting GOR IV under Secondary structure prediction tool to open the query form. Paste the query sequence into the sequence box and click the Submit button. The result is returned showing the query sequence with the corresponding predicted conformations (c, h, e, and t for coil, helix, extended strand, and turn, respectively), summarized content (%) of conformations, and conformational profiles (Figure 12.6). 

The 3D-PSSM (Kelley et ah, 2000) server at http //www.bmm.icnet.uk/ 3dpssm/ offers online protein fold recognition. On the submission form, enter your e-mail address and a one-line description of the query protein, then paste the query sequence into the sequence box and click the Submit button. The query sequence is used to search the Fold library for homologues. You will be informed of the URL where the result is located for 4 days. The output includes a summary table (hits with statistics models that can be viewed with RasMol classifications and links) and fold recognition by 3D-PSSM with a printout as exemplified in Figure 12.13. The alignment displays consensus sequence, secondary structures (C for coil, E for extended, and H for helix), and core score (0 for exterior to 9 for interior core). 

The results are presented in terms of bibliographic and chemical text, 2D chemical diagrams, 3D structure diagrams at the molecular or extended crystal structure levels, and also as tables of geometrical parameters for each located substructure or chemical fragment. The search query is via... 

Tripos mainly contains StereoPlex that is designed specifically to address the need for additional stereomers in your 3D databases. StereoPlex functions as a 3D database-extender and can be used either by itself or as a CON CORD pre-processor. What is more, when compounds have more than a single stereocenter, StereoPlex actually increases the 3D shape diversity of the databases, thus becoming a data-hase-diversifier. While diastereomers and enantiomers often look the same to distance-based pharmacophores or database queries, to biological receptors they are as different as night and day. StereoPlex has several features ... 

The Process Data Warehouse, as described in this subsection, has been implemented using the deductive object-base ConceptBase [204]. The lifecycle model CLiP was realized in ConceptBase (see Subsects. 1.3.4, 2.1.3, and 2.2.3), while the tool environment uses the interfaces offered by the CAPE-OPEN initiative to integrate physical properties, mathematical models, and simulators. Subsequently, it will be shown how this setup is used in an example scenario. In this scenario, the services offered by the PDW Query Assistant are used by the PRIME process integrated environment (cf. Subsect. 3.1.3) for extended situation analysis. 

The warehouse itself contains several sub-meta databases that are queried during the processing of this request for extended situation analysis ... 

Probabilistic attribute correspondences extend attribute correspondences by generating multiple possible models, modeling uncertainty about which one is correct by using probability theory. Such probabilities can then be combined to represent possible schema mappings, based on which query processing can be performed. 

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