Search, substructure

To seat ch for available starting materials, similarity searches, substructure searches, and some classical retrieval methods such as full structure searches, name searches, empirical formula searches, etc., have been integrated into the system. All searches can be applied to a number of catalogs of available fine chemicals (c.g, Fluka 154]. In addition, compound libraries such as in-housc catalogs can easily be integrated. 

Searches on the text and numeric values are performed by the ORACLE search engine using the Chem-X user-interface. This allows the user transparent access to ORACLE as well as to search substructure and text/numeric values at the same time. The details of how this is implemented are outside the scope of this publication. 

Molecular descriptors play a fundamental role in chemistry, pharmaceutical sciences, environmental protection policy, health research, and quahty control, being the way molecules, thought of as real bodies, are transformed into numbers, allowing some mathematical treatment of the chemical information contained in the molecule. Therefore molecular descriptors allow us to find - structure/response correlations and perform - similarity searching, - substructure searching, etc. 

Baldi, Benz et al, 2007]. In effect, in folded vectors, different fragments can set the same bit causing fragment collisions. In any case, this does not affect the effectiveness of screening because false positives can be returned for an atom-by-atom matching, but compounds with the searched substructure vdll never be rejected. 

Before addressing some aspects of, broadly speaking, ligand-receptor interactions, a critical evaluation of protein structure determination was felt in order. This is then followed by accounts of docking and scoring, pharmacophore identification 3D searching, substructure searching, and molecular descriptors. 

Ehrlich HC, Rarey M. Searching substructures in fragment spaces. J Chemoinf 2011 3(Suppl 1). 

The major capabilities of chemical information retrieval today are formula searches, substructure searches, exact match searches, and sequence match, homology, and subsequence searches. (Name, textual, and data searches are ignored in this note, as essentially belonging to the realm of text and data retrieval.)... 

By using exact molecules as queries in these searches, users do not have to learn a complex query language and, more importantly, can avoid any bias based on preconceptions which is inherent in substructure searching. Substructure searching, however, is subsequently used to fine-tune the results and to reduce the initially large number of hits from the similarity search to manageable size. The result is a synthesis tree consisting of many reasonable pathways, one of which is shown in... 

Regarding structural databases on the Internet, the WWW chemical structures database established by the Computer Chemistry Center at the University of Erlangen should be mentioned. Currently this database contains more than 2250 chemical structures collected automatically from the Internet, complete with information about the referring html pages. The search operations supported in this database include full structure search, substructure search, formula-oriented searches, and queries on names, CAS-Numbers,... 

A structure search of chemical substances can be performed in the chemical structure databases. The structure query can be input using a graphical structure editor. The following search methods are possible, depending on the type of structure database. The structure search capabilities depend on the software system. Here, the focus is on the implementation of STN International exact structure search, family search, substructure search, similarity search, generic (Markush) search, and reaction search. 

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