Chemical literature databases

Moore RE, Pettus JA Jr, Doty MS (1968) Dictyopterene A, an odoriferous constituent from algae of the genus Dictyopteris. Tetrahedron Lett 46 4787 1790 Munro MHG, Blunt JW (2005) MarinLit, a marine chemical literature database, version 12.5. 

Munro, M. H. G. and Blunt, J. W., MarinLit, a marine chemical literature database, version 10.4, Marine Chemistry Group, University of Canterbury, Christchurch, NZ, 1999. 

A better way to obtain the information we seek is to use chemical literature databases. Several such databases exist. These resources can be used for retrospective searches of mentions of any given program, vendor, method, or other term. It is also highly fitting to use a computerized technique (database searching) in our study of computational chemistry. 

There were a number of practical and theoretical issues to be addressed. A key scientific question was whether fixation in formalin modified antigens in a reversible or irreversible manner. To be more specific, was there any theoretical or prior scientific evidence that the effects of formalin fixation on proteins could be reversed, and if reversed, was the structure of protein restored to a sufficient degree for recovery of antigenicity With these key questions in mind, one of the authors (Shi) spent many days and nights in 1988 searching the chemical literature under somewhat adverse conditions, with a second job as an apprentice in a supermarket, and prior to the increased efficiency of such searches that is afforded today by the Internet and online databases. The answer was finally found in a series of studies of the chemical... 

The topics of the present presentation is closest to that of the monograph written by Torssell (4). Therefore, the aim of this chapter is to update the information concerning nitrile oxides published after the monograph (4). The literature was followed by Chemical Abstracts database (1988—2001) and indices from Vol. 136 (2002) till Vol. 144 (2006). As to the period 1988-2002, references will be given practically only to data omitted in Reference 5. 

Consider a molecular structure, which is the most important unifying information model in chemistry. Molecular structures appear in knowledgebases that represent catalogs of commercially available chemicals, pharmacology of named drugs, natural sources of bioactive molecules, protein-ligand interactions, measured molecular bioactivities, metabolic pathways, abstracted research literature, databases of synthetic reactions, and so on. 

The DNP (Chapman HaU/CRC Dictionary of Natural Products) is a comprehensive literature database of around 170 000 isolated natural products from various sources and provides names, chemical structures, CAS registry numbers, extensive source data, uses and applications. 

Budgeting. Changes in the storage and retrieval of chemical information require that libraries anil information centers now consider not only what should be purchased but also what monies should be allocated for the purchase of information in nonprint formats such as CD-ROMs (compact disk read-only memory and on-line databases. Coupled with this is budgeting for the cost of hardware and software to enable the rapid and cost-effective delivery of needed information. The geometric increase in sources, both printed and on-line, has increased ihe role of the information specialist as an expert in the delivery of chemical information. Retrieval from increasingly diverse and complex sources becomes the paramount issue for searchers of chemical literature in the 1990s. 

There are a remarkable number and diversity of activities that have been modeled successfully. The activity to be modeled may be a toxicity to an environmental organism or to man, the fate of a pollutant in an ecosystem, or the pharmacokinetic properties of a xenobiotic in man. To model any of these activities, relevant biological data for the endpoint are required. Chapter 2 describes how toxicological and fate information for chemicals may be obtained from external sources such as the open literature, databases, and the Internet. QSAR developers may also have their own data to model. 

In the area of chemical literature information, the largest databases are produced by the Chemical Abstracts Service (CAS) of the American Chemical Society (ACS). As detailed on their website (www.cas.org), their principal databases are the Chemical Abstracts database (CA) with 16 million document records (mainly abstracts of journal articles and other literature) and the REGISTRY database with more than 28 million substance records. In an earlier volume of this series, we discussed CAS s SciFinder software for mining these databases. SciFinder is a tool for helping people formulate queries and view hits. SciFinder does not have all the power and precision of the command-line query system of CAS s STN, a software system developed earlier to access these and other CAS databases. But with SciFinder being easy... 

A survey on 3D-QSAR literature (Oprea 2004) reported more than 1100 entries in the Chemical Abstracts database on CoMFA, 3D-QSAR, and related keywords. For CoMFA alone, 586 publications between 1988 and 2001 demonstrate its wide distribution and applicability. As the number of potential targets in drug discovery is steadily increasing, it is likely that 3D-QSAR models and methodologies will continue to be developed in the future. Successful applications were not only reported to understand target related affinity but also for some ADME relevant targets... 

The database contains CAS Registry Numbers, structures, and names for substances reported in the chemical literature covered in CA, in addition to substances registered from special collections, for governmental and industrial organizations, and for individual requesters. CAS Registry Numbers are also assigned to sequences such as DNA and proteins. 

Chemical-physical data, literature Database catalog for chemists http //www.chemie- datenbanken.de... 

In addition to the published literature, a chemical shift database is being developed by Advanced Chemistry Development (AC D/Labs) that can be used interactively by an investigator both to predict chemical shifts for a molecule being investigated and to search the database by a multitude of parameters, including structure, substructure, and alphanumeric text values. This database is accessible in the NNMR software package offered by ACD/Labs and presently contains data on more than 8800 compounds with over 20 700 chemical shifts. Examples of the use of the NNMR database will be presented later in this chapter. 

A literature database well suited for obtaining the information we seek is the Current Journals of the American Chemical Society (CJACS) file. Like the CA file, CJACS is produced by the CAS and is searchable through the STN International network. The CJACS database has the advantages of being large (145,001 papers) and interdisciplinary, as well as covering some of the journals with the highest impact - on chemistry. The records in the database include not only abstracts, but also the full text of the articles and all the references and... 

One of the most thorough ways of retrieving data from the literature is through searching databases of full articles. We find, from a detailed analysis of CAS s CJACS database, year-by-year increases in mention of many computational chemistry programs. Because of the sheer size of CJACS (145,001 articles), we expect it to be quite representative of the chemical literature as a whole. In addition, we have shown corroborative data from CAS s CJWILEY database and from the MMCC Results newsletter. 

Chemical Abstracts. A weekly publication of the American Chemical Society that consists of research articles and patents in all major fields of chemistry throughout the world. It is completely computerized, including the ability to draw chemical structures as the basis for a search of the database, and available in various forms from several computerized services. It is the most indispensable information source in chemical literature and is the largest scientific abstract journal in the world. For further information, see Appendix II. 

ChemSpider currently searches over 14 million compounds in multiple chemical structure databases. These include databases of curated literature data, chemical vendor catalogs, molecular properties, enviromnental data, toxicity data, analytical data, and so on. ChemSpider intends to aggregate into a single database all chemical structures available within open access and commercial databases and to provide the necessary pointers from the ChemSpider search engine to the information of interest. This service will allow users to either access the data immediately via open-access links or have the information necessary to continue their searches into commercially available systems. 

Once fractionation has led to some physical characteristics of the active component, such as UV spectra or putative molecular weight, another literature search can be executed. During the isolation and structure identification of the zaragozic acids (also known as squalestatins) (75), a literature search of the Chemical Abstracts database was carried out within hours of isolating sufficient material to obtain a COSY spectrum, since the two substructures (A and B) were readily identified from these data (see Fig. 12). When the Chemical Abstracts search revealed that no known compounds contained either of these substructures, it was obvious that the compound was novel and therefore patentable. It was several more days before enough NMR and MS experiments had been carried out and an exhaustive structure determination completed, at which point the truly novel 2,8-dioxabicyclo[3.2. l]octane-3,4,5-tricarboxylate core of the zaragozic acids could be searched for in Chemical Abstracts and shown to be unprecedented in the natural product literature. 

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