IDENT Complete Structure Search

Usually the secondary structure units (a helices and 3 strands) are constructed first. Next one must find loops with an appropriate distance between the ends so that the gaps in the modeled protein can be filled in. These loops can be found by searching the Brookhaven Protein Data Bank ° or a subset thereof. i Seldom will a single protein crystal structure suffice as a source for the pieces rather, segments from several different known structures must be combined. Substitution of individual residues is also used when complete structure identity is not achieved by searching for appropriate segments. The model is usually refined by energy minimization and molecular dynamics. It helps if there is information available to verify key aspects of the final model, partic-... 

ECR-1 is a true boundary phase between two compatible structures - mazzite and mordenite - which normally crystallize with greatly disparate Si/Al ratios (3.4 and >5 respectively). Yet ECR-1 has an Si/Al ratio identical to mazzite, even though half of its component sheets are structurally characteristic of mordenite (in the structure proposal). This compositional incompatibility is further reflected in the almost complete lack of mixtures of mazzite with mordenite in the experiments so far completed. The ongoing search for ECR-1 with mordenite overgrowths is therefore an important objective in the understanding of crystallization mechanisms in this system, with particular interest in the possible compositional variation between all three component zeolites. 

Obtaining a structural model fi-om the analysis of potentially isostructural compounds with partially or completely different chemical composition but identical or similar stoichiometry. The search for isostructural compounds may be conducted using a digitized powder pattern, unit cell dimensions, stoichiometry, and/or other suitable parameters. ... 

Library searching techniques are of two kinds identity searches and similarity searches. Identity searches (i.e., searches requiring an exact match between the query and the reference) are successful only if the sought spectrum or structures are already in the reference library. If not, the search fails completely. In contrast, similarity searches depend on the metrics introduced into the representation of the spectra or structures. The metrics and consequently the distance or the similarity measure between the query object and the reference depend on the problem being studied hence, the results obtained on the basis of similarity are not directly comparable when the problems are from different fields. 

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