Database structure viewers

ChemDraw plug-in This is claimed as being more than a mere structure viewer or a slow Java applet, rather it runs as fast and is as familiar as the regular ChemDraw application. Available without charge, it enables searching of web databases by structure or substructure, and viewing of ChemDraw documents that others have placed on the web. http //www.camsoft.com... 

The functionality required for an ELN to handle these structures is a specialized structure editor allowing creation and visualization of residues, definition of residues as real structures, and combined search for substructures in both the compound and the residue. Some additional features in the structure viewer help to mark and emphasize residues of the structure, allow overlapping residues, and label residues. A flag indicates whether the residues are displayed in the current context or not. If more than one residue is available, it is possible then to show or hide individual residues of a structure. The structure editor may be independent of a primary editor that is able to handle complete structures that is, structures are created with an external standard editor, whereas residue definitions are performed with an embedded tool. Since most databases are not designed for storing incomplete information, an ELN has to provide an internal format to store incomplete structures. In fact, it stores every complete part of a structure in a conventional database and keeps the additional information about the missing parts. 

The results of a structure or reaction query are displayed in a hit list, ideally within an ELN software. The user can then create a new section in the electronic scientific document using any structure from the hit list, including metadata delivered by the database. By transferring the structure, an additional unique identifier from the external database needs to be kept that is, the created section has a hyperlink to the external system that allows opening the default structure viewer directly from the section. 

The QCRNA database is viewable and searchable with a web browser on the internet and it is also contained as a MySQL database that is easily incorporated with parameter optimization software to allow for the rapid development of specific reaction parameters. Molecular structures can be viewed with the JMOL [47, 48] or MOLDEN [49, 50] programs as viewers for chemical MIME types. If the web browser is JAVA-enabled, then the JMOL software will automatically load as a web applet. Both programs allow the structure to be manipulated, i.e., rotated, scaled, and translated, and allow for measurement of internal coordinates, e.g., bond lengths, angles, and dihedral angles. Similarly, animations of the vibrational frequencies are available and can be viewed with either program. 

It should also be noted that besides all these features, there are 3 analysis tools that are useful for a user to understand each framework in this database. TOTOPOL is a topological analysis tool CIF-2-POWD is an online program to calculate the simulated powder XRD pattern and Sphere Viewer is a program that computes and displays the spheres which can fit inside a framework structure. A user could use these tools directly... 

Illustrations with organic structural formulae have been used widely. In depicting sugar rings. Mills formulae have been used if the conformation is not known with confidence, otherwise conformational structures are drawn. Ribbon diagrams of various carbohydrate-active proteins with known structures are available from protein databases. Their reproduction in this book would have increased its cost and, at a time when all beginning researchers have Web access, only marginally increased its usefulness. If the reader wants to know what, say, a GH6 cellulase looks like, he or she should go to CAZy, the wonderful resource for the whole scientific community started by Bernard Henrissat and maintained by him and Pedro Coutinho, and click on the links in the 3D column. The protein can then be viewed in various downloadable viewers. 

A complete application programming interface is available for MMDB as part of the NCBI toolkit, containing a wide variety of C code libraries and applications. Both an ASN.l input/output programming interface layer and a molecular computing layer (MMDB-API) are present in the NCBI toolkit. The NCBI toolkit supports x86 and alpha-based Windows platforms, Macintosh 68K and PowerPC CPUs, and a wide variety of UNIX platforms. The three-dimensional structure database viewer (Cn3D) is an MMDB-API-based application with soince code included in the NCBI toolkit. 

Figure 3 Accessing the WWW chemical structures database through the Web Interface. The input structure is vanillin, queried by a full-structure search. The hit list and one selected entry from the list are displayed in separate windows. Below the shown part of the selected entry, a Java molecule viewer displaying the structure in 3D and a clickable map of Web pages referring to the entry are hidden...

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