Computational Structural Genomics

Today we are approaching a historic intersection between biology and society. Because of a major investment by society in biological research, funding the human genome project and the study of other genomes, biology has been transformed; and now in the 21st century medical practice will be equally affected. The revolution in basic biological science provides an opportunity to improve health care at reduced cost and, beyond that, to enhance the quality of life and productivity of humankind. Advanced computing is an essential requirement for reaching the goals for the human genome project.

The human genome project is an international research effort with the goal of discovering the recipe for life—determining the sequence of all human DNA, 3 billion base pairs—and identifying the 100,000 human genes contained therein. DNA contains all of our genetic instructions, giving us blue eyes rather than brown, and resistance to certain diseases and sensitivity to others. The human genome project was undertaken to provide us with the information necessary to treat more than 4000 genetic diseases that afflict mankind, as well as to provide information on the much larger set of diseases in which genes play a role.

The project will also provide information on how humans grow, how the body works in health and fails in disease, and on the tendency to inherit certain diseases or be susceptible to environmental damage. Due to the genome project, spectacular progress has already been made against cystic fibrosis and muscular dystrophy, both fatal genetic diseases in children. Researchers have identified the flaws in genes that dispose people to heart disease, diabetes, arthritis, and breast and colon cancer. Indeed, the project has already created a source book for biomedical science and the extraordinary, even unexpected progress, has transformed biological research and led to the urgent need for advanced information technology and high-end computing resources. Information technology will allow physicians to make more precise clinical diagnoses and public health predictions, chemists and pharmacologists to design more effective drugs, and biomedicine to prevent many painful disorders, and may one day even allow the correction of malftmctioning genes.

Genes code for protein molecules that are the "machines" of life. Each day the human body requires a fresh crop of protein molecules in the right quantities at the right places and the right times—antibodies to fight bacteria and other invaders, hemoglobin to carry oxygen through the bloodstream for use in cells, and hormones to deal with stress and control many physiological processes. To understand and exploit the molecular "recipes" coded in the DNA, we must both understand the genes themselves and the proteins they code.

Computational structural genomics is the use of information technology and computers to understand DNA sequences—to use our growing knowledge to tell us where new genes are and how they are controlled—and to understand how genes dictate the structure and thus the function of proteins. A major question for biology is to understand the relationship of sequence, structure and function of proteins. Sophisticated simulation studies along with new techniques for information management and visualization, will provide the means to answer this question.