Computer in biochemical research

The computer has become an essential tool in biochemical research. A computer may be used for the routine jobs of word processing and data collection and analysis. In addition, if a computer is connected to the Internet, then it may be used for biochemical literature searching, accessing information about nucleic acid and protein sequences, predicting protein structure, and seeking research methodology. In this experiment, students will be introduced to all of these skills in bioinformatics. 

Tris is short for tris(hydroxymethyl)aminomethane. This weak base is widely used in biochemical research for the preparation of buffers. It offers low toxicity and a pK, (5.92 at 25°C) that is convenient for the control of pH in clinical applications. A buffer is prepared by mixing 0.050 mol of tris with 0.025 mol of HCl in a volume of 2.00 L. Compute the pH of the solution. 

The facile conversion of sequences into 3D structures that can be displayed and manipulated on the computer screen (molecular graphics) has greatly improved molecular modeling as an essential tool in biochemical research and teaching. The ID sequences can be converted into 2D structural representations by the use of ISIS Draw, which can be down-... 

B. R. Kowalski, "Pattern Recognition in Chemical Research," in C. E. Klopfenstein and C. L. Wilkins, eds.. Computers in Chemical and Biochemical Kesearch Vol. 2, Academic Press, New York, 1974. 

In combination, the book should serve as a useful reference for both theoreticians and experimentalists in all areas of biophysical and biochemical research. Its content represents progress made over the last decade in the area of computational biochemistry and biophysics. Books by Brooks et al. [24] and McCammon and Harvey [25] are recommended for an overview of earlier developments in the field. Although efforts have been made to include the most recent advances in the field along with the underlying fundamental concepts, it is to be expected that further advances will be made even as this book is being published. To help the reader keep abreast of these advances, we present a list of useful WWW sites in the Appendix. 

The scope of the use of mass spectrometry in the protein analysis has grown enormously in the past few decades. MS has become an important analytical tool in biological and biochemical research. Its speed, accuracy and sensitivity are unmatched by conventional analytical techniques. The variety of ionization methods permits the analysis of peptide or protein molecules from below 500 Da to as big as 300 Da (Biemann 1990 Lahm and Langen 2000). Basically, a mass spectrometer is an instrument that produces ions and separates them in the gas phase according to their mass-to-charge ratio (m/z). The basic principle of operation is to introduce sample to volatilization and ionization source, and then the molecular fragments from the ionization of the sample are detected by various kinds of detector and the data are analyzed with computer software. 

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... 

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