Computer — Personal Searching

Research articles of interest to biochemists may appear in many types of research journals. Research libraries do not have the funds necessary to subscribe to every journal, nor do scientists have the time to survey every current journal copy for articles of interest. Two publications that help scientists to keep up with published articles are Chemical Titles (published every 2 weeks by the American Chemical Society) and the weekly Current Contents available in hard copy and computer disks (published by the Institute of Science Information). The Life Science edition of Current Contents is the most useful for biochemists. The computer revolution has reached into the chemical and biochemical literature, and most college and university libraries now subscribe to computer bibliographic search services. One such service is STN International, the scientific and technical information network. This on-line system allows direct access to some of the world s largest scientific databases. The STN databases of most value to life scientists include BIOSIS Pre-views/RN (produced by Bio Sciences Information Service covers original research reports, reviews, and U.S. patents in biology and biomedicine), CA (produced by Chemical Abstracts service covers research reports in all areas of chemistry), MEDLINE, and MEDLARS (produced by the U.S. National Library of Medicine and Index Medicus, respectively cover all areas of biomedicine). These networks provide on-line service and their databases can be accessed from personal computers in the office, laboratory, or library. Some... 

The inversion of the Drude equations, that is the estimation of unknown thicknesses or optical constants from ellipsometric measurements, relies upon the application of computer-intensive search and optimization methods, which are well within the capabilities of personal computers. The software for solving a wide variety of film problems is now available as part of the instrumentation package from a good number of ellipsometer manufacturers. This has resulted in the fast-widening scope of ellipsometry as reflected in the number of publications in which the technique is dominant. 

Scientists are forever searching for electronic components like transistors that will perform their function with minimum production of heat. In early versions of personal computers the heat produced by the components could not be dissipated by natural means and fans were used to force the heat to the surroundings. Most contemporary personal computers, including laptops, rely on removing heat by natural means and do not require fans. 

In the last decade, for many toxicologists the on-line literature search has changed from an occasional, sporadic activity to a semicontinuous need. Usually, nontoxicology-related search capabilities are already in place in many companies. Therefore, all that is needed is to expand the information source to include some of the data bases that cover the types of toxicology information one desires. However, if no capabilities exist within an organization, one can approach a university, consultant, or a private contract laboratory and utilize their on-line system at a reasonable rate. It is even possible to access most of these sources from home using a personal computer. The major available on-line data bases are described in the following. 

The lists of references at the ends of chapters are provided to encourage readers to look at original research articles. The lists are neither complete nor critically selected, but they do increase the information given in this book many-fold. I apologize for the important papers omitted. However, the references that are here will help a student to get started in reading the literature. Each reference contains other references and names of persons active in the field. By searching recent journal indices or a computer database it is easy to find additional articles by the same authors or on the same subject. 

Most of the chemists will agree that chemical structure is a common denominator in the majority of chemical work and that it seems naturally to discuss the ways how chemical structures can be handled (input, output, displayed, compared, searched, ranked, etc.) by computers (ref. 1) in general and by personal computers in particular. 

The main purpose of FFT or FHT of discrete spectra is not the reduction of storage space because a tabular representation of peaks would be usually short enough (see Chapter 4). Nevertheless, an efficient (w ith a respect to the computation time) manipulation and comparison of spectra calls for short and uniform representation and the use of reduced transforms is justified and helpful, especially w hen searching spectral collections resident personal computers. 

Another tedious and time-consuming task can be literature searches. We find these searches can be handled quite easily by computer. A person skilled in searching the many databases available can do so in a very short time. 

There are disadvantages too. Some databases do not include all of the material available in conventional form for example, much of the early Chemical Abstracts is not available on-line. Another problem is that the software for on-line searching is relatively complex, so it is more difficult to learn and, as a result, on-line searches by inexperienced users can be unreliable. The increasing use of personal computers and graphical input and output have made database searching much easier but a good understanding of the software is stUl essential. Finally the cost of hardware, software, consumables, and the searches themselves, can be considerable. 

A number of software and database vendors provide programs and database systems to implement representation, registration, and searching of chemical information in a corporate environment. Some of these vendors have smaller personal chemical database systems that support registration and searching on a personal computer. A handful of academic and public domain systems are also available. Finally, an increasing number of chemical information systems are being made available on... 

The sequence of a protein of interest can be compared with all other known sequences to ascertain whether significant similarities exist. Does this protein belong to one of the establishedfamiliesl A search for kinship between a newly sequenced protein and the thousands of previously sequenced ones takes only a few seconds on a personal computer (Section 7.2). If the newly isolated protein is a member of one of the established classes of protein, we can begin to infer information about the protein s function. For instance, chymotrypsin and trypsin are members of the serine protease family, a clan of proteolytic enzymes that have a common catalytic mechanism based on a reactive serine residue (Section 9.1.4). If the sequence of the newly isolated protein shows sequence similarity with trypsin or chymotrypsin, the result suggests that it may be a serine protease. 

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