Structure retrieval/generation

Structure retrieval or generation Crystal structures of organic compounds can be found in the Cambridge Crystallographic Datafiles (http //www.ccdc.cam. ac.uk/). Those that does not exist may be generated by 3D rendering software. The 3D structural coordinates of biomacromolecules can be retrieved from Protein Data Bank (http //www.rcsb.org/pdb/). 

The program MIMUMBA starts from an arbitrary 3D structure and generates other conformations by changing individual torsion angles to values which correspond to different conformational preferences [968] the distribution profiles of allowed and preferred torsion angles are retrieved from corresponding partial structures in the Cambridge database of crystal structures [141]. 

Therefore, we can obtain data from ORACLE based upon structural retrievals. It also allows us to write information to ORACLE databases from a MACCS application and temporarily switch to an ORACLE relational application if we desire. This latter capability provides a link to ORACLE tools from MACCS. An additional aspect of this link is to use the MACCS interactive display to do ad hoc queries of the ORACLE databases. This allows one to generate lists of chemical entities based upon the... 

Fragment screen generation for structure retrieval and. spectral analysis (see Structure and Substructure Searching)... 

Chemoinformatics refers to the systems and scientific methods used to store, retrieve, and analyze the immense amount of molecular data that are generated in modern drug-discovery efforts. In general, these data fall into one of four categories structural, numerical, annotation/text, and graphical. However, it is fair to say that the molecular structure data are the most unique aspect that differentiate chemoinformatics from other database applications (1). Molecular structure refers to the 1-, 2-, or 3-D representations of molecules. Examples of numerical data include biological activity, p/C, log/5, or analytical results, to name a few. Annotation includes information such as experimental notes that are associated with a structure or data point. Finally, any structure... 

The result of any retrieval command in MAECIS is a set of chemical structures which is referred to as the "current set". If a second retrieval is made, the current set is moved into another internal storage area and is referred to as the "prior set". In this way, MAECIS automatically keeps track of at least two retrievals for the user. However, it is often necessary to establish several sets of molecules during a single computer session. In MAECIS, any number of sets can be retained using a SAVE command which allows the user to name and save any set of molecules created by a retrieval command. Any stored set in MAECIS can also be referenced in a subsequent FIND command. Thus, new sets can be generated from old sets through the find command s boolean operations. Sets retained with the SAVE command are in temporary memory. To make them permanent, the STORE and RESTORE commands are available to move sets to and from permanent disk files. 

The Structure of DNA Elucidation of the three-dimensional structure of DNA helped researchers understand how this molecule conveys information that can be faithfully replicated from one generation to the next. Tb see the secondary structure of double-stranded DNA, go to the Protein Data Bank website (www.rcsb.org pdb). Use the PDB identifiers listed below to retrieve the data pages for the two forms of DNA... 

It is the set of methods for representing, sorting, manipulating and retrieving information about chemical substances that distinguishes the techniques of chemical information handling from those of other disciplines. Chemical literature emphasizes the detailed structural characteristics of chemical substances. This is illustrated by the fact that for the 392,000 documents abstracted in 1975 in CHEMICAL ABSTRACTS, 1,514,000 chemical substance index entries were generated. Of these chemical substance index entries, 368,000 corresponded to substances which were reported for the first time in 1975. 

A Chemically Oriented Information Storage and Retrieval System II. Computer Generation of the Wiswesser Notation of Complex Polycyclic Structures," Journal of Chemical Documentation, (3), 133-138 (1968). 

---