Artificial Intelligence and Molecular Biology (American Association for Artificial Intelligence)
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The enormous amount of data generated by the Human Genome Project and other large-scale biological research has created a rich and challenging domain for research in artificial intelligence. These original contributions provide a current sampling of AI approaches to problems of biological significance; they are the first to treat the computational needs of the biology community hand-in-hand with appropriate advances in artificial intelligence. Focusing on novel technologies and approaches, rather than on proven applications, they cover genetic sequence analysis, protein structure representation and prediction, automated data analysis aids, and simulation of biological systems. A brief introductory primer on molecular biology and Al gives computer scientists sufficient background to understand much of the biology discussed in the book.Lawrence Hunter is Director of the Machine Learning Project at the National Library of Medicine, National Institutes of Health.
of overviews; I can only begin to convey the depth, variety, complexity and stunning beauty of the universe of living things. Much of what follows is not about molecular biology per se. In order to 2 ARTIFICIAL INTELLIGENCE & MOLECULAR BIOLOGY explain what the molecules are doing, it is often necessary to use concepts involving, for example, cells, embryological development, or evolution. Biology is frustratingly holistic. Events at one level can effect and be affected by events at very
exploited by cell mechanisms. The fact that the conformation of the DNA can have a biological effect over and above the sequence it encodes highlights an important lesson for computer scientists: there is more information available to a cell than appears in the sequence databases. This lesson also applies to protein sequences, as we will see in the discussion of post-translational modification. Now that we have covered the basic structure and function of proteins and nucleic acids, we can begin
gene into the vector and the uptake of the vector by the target cells are effective only a fraction of the time. Fortunately, cells and vectors are small and it is relatively easy to grow a lot of them. The process is applied to a population of target cells, and then the resulting population is screened to identify the cells where the gene was successfully inserted. This can be difficult, so many vectors are designed to facilitate screening. One popular vector, pBR322, contains a naturally
produce an advantageous variation than random ones. Although you wouldn’t necessarily recognize it as sex when looking under a microscope, even some Bacteria exchange genetic material. How and when sexual recombination first evolved is not clear, but it is quite ancient. Some have argued that sexual reproduction was a necessary precursor to the development of multicellular organisms with specialized cells (Buss, 1987). The advent of sex dramatically changed the course of evolution. The new
should probably represent these structural units as vectors, linear combinations of basis vectors representing physical and chemical characteristics, like molecular weight, steric configuration, charge, magnetic dipole, and hydrophobicity [Nakai, et al 1988; Hunter, 1992]. Phylogeny is another source of information. How can knowledge of the structure and sequence of one molecule be used to predict the structure of another molecule whose sequence is homologous or whose function is the same? Major