Chemical structure browsing

Sandy Lawson s contribution on chemical structure browsing (Chapter 4) may seem peripheral to the main topic of the symposium, but the algorithm he employs could, he hopes, be used for data bases other than Beilstein in future. 

SciFinder at http //www.cas.org/SCIFINDER/scicover2.html is an easy-to-use desktop research tool that allows the user to explore research topics, browse scientific journals, and access information on the most recent scientific developments. SciFinder Scholar is a desktop research tool designed especially for use by students and faculty to easily access the information in the CAS databases. With either tool, one can search Chemical Abstracts and the CA Registry by author name, research topic, substance identifier, chemical structure, or chemical reaction. 

SciFinder provides an easy interface to search efficiently scientific information without needing to learn complicated issues of database searching of chemical information. Tutorials are available on the web for using Explore by Research Topic, how to set up a Keep Me Posted alert to get breaking news, Browse the Table of Contents of journals, and other SciFinder features. Explore by Chemical Structure allows one to find substances based on their structure to display its physical properties, as well as information on obtaining the substance from commercial sources. CAS STN and SciFinder are considered the most extensive source of chemical information, particularly for information from the patent literature. 

In the Data Analysis Wizard (MetaDrug ) window (step 1, Fig. 1) click In Browse under Upload CDX, SDF or MOL file and open an appropriate chemical structure file. If multiple structures are to be batch-uploaded from an SDF file, individual compound reports will be generated for each structure... 

Bawden, D. Browsing and Clustering of Chemical Structures. In these Proceedings. 

CHE CHEMICAL STRUCTURE FILES NOV NOVELTY CHECK BRO BROWSE SIMILARITY SEARCH QSM SCREENING HISTORIES DAT BIOLOGICAL TESTING DATA QFC FCD TEXT SEARCH QCD CSDB TEXT SEARCH... 

Bawden D. Browsing and Clustering of Chemical Structures . In Chemical Structures. The International Language of Chemistry Warr W.A., Ed. Springer-Verlag Berlin, 1988 pp. 145-150. 

Offline preparation and presentation of chemical structure graphics is now possible on a PC using a variety of query editor programs (7), such as those listed in Figure 3. In most cases these are specific to a single system, and use a proprietary format for transmission of the query structure between the PC and the mainframe computer. For example, STN Express allows query structures to be built offline and then, after connection to STN, uploaded and searched against the STN online structure files. Retrieved structures can be downloaded onto the PC and browsed offline in STN Express. Similarly, CHEMLINK is now available for Telesystemes-DARC, while in the case of in-house systems, ChemBase provides similar capabilities for MACCS. 

If you do not have a subscription, you can still view the tables of contents of the volumes and the abstract of each article by going to the SpringerLink Home-page, clicking on Browse by Online libraries , then Chemical Sciences , and finally choose Structure and Bonding. 

Browse through three articles in Chemical Research in Toxicology or the Journal of Agricultural and Food Chemistry. For each article, copy and paste into a text document one sentence from each IMRD section that is consistent with the hourglass structure. Examine each group of four sentences. Is the hourglass structure apparent in these four sentences Explain. 

Browse through three articles in one of the following journals The Journal of Organic Chemistry, Analytical Chemistry, Environmental Science Technology, or Chemical Research in Toxicology. Flow well do the articles adhere to the move structure illustrated in hgure 4.1 ... 

Click on the Convert SMILES button to perform the conversion of the linear SMILES strings into 3D coordinates (SDF format). To browse automatically, click the Start Visualizer button for the systematic viewing of the 3D molecular structures from the chemical library (Fig. 18.3). 

Figure 3.6 shows 12 structures that may correspond to the abbreviation DPA. Six of them can be output by the ACD/Name to Structure software package, and six more were found by browsing the Internet. Note that even a specific context cannot guarantee an exact meaning. For example, both structures 3 and 8 were found in publications about coordination compounds. In general, chemical abbreviations are not unique and can rarely be distinguished from other trivial names except for the rather weak criterion that all letters are capitalized. We can conclude that conversion of any trivial name shorter than about five or six characters is not safe. A few rarer exceptions do exist, but this is a very short list. Examples include reserved abbreviations such as those for dimethyl sulfoxide (DMSO) and ethylenediaminetetraacetic acid, EDTA. 

The full nomenclature can be browsed at http //www.chem.qmul.ac.uk/iubmb/enzyme/.) Like all proteins, enzymes are made as linear chains of amino acids that fold to produce a three-dimensional product. Each unique amino acid sequence produces a specific structure, which has unique properties. Enzymes can be denatured - that is, unfolded and inactivated - by heating or by chemical denamrants, which disrupt the three-dimensional structure of the protein denaturation may be reversible or irreversible. 

---