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Calculating the Secrets of Life: Contributions of the Mathematical Sciences to Molecular Biology (1995)

Chapter: Chapter 9 Folding the Sheets: Using Computational Methods to Predict the Structure of Proteins

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Suggested Citation:"Chapter 9 Folding the Sheets: Using Computational Methods to Predict the Structure of Proteins ." National Research Council. 1995. Calculating the Secrets of Life: Contributions of the Mathematical Sciences to Molecular Biology. Washington, DC: The National Academies Press. doi: 10.17226/2121.
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FOLDING THE SHEETS: USING COMPUTATIONAL METHODS TO PREDICT THE STRUCTURE OF PROTEINS 236 Chapter 9— Folding the Sheets: Using Computational Methods to Predict the Structure of Proteins Fred E. Cohen University of California, San Francisco In principle, the laws of physics completely determine how the linear sequence of amino acids in a protein will fold into a complex three-dimensional structure with useful biochemical properties. In practice, however, predicting structure from sequence remains a major unsolved problem. In this chapter the author outlines current approaches to structure prediction. The most fruitful approaches are not based on physical simulations of the folding process, but rather exploit the conservative nature of evolution. Using statistical methods, pattern matching techniques, and combinatorial problem solving, protein structure prediction is becoming steadily more tractable. At the crossroads of physics, chemistry, biology, and computational mathematics lies the protein folding problem: How does a linear polymer of amino acids assemble into a three-dimensional object capable of executing a precise chemical function? Implicit within this question are both kinetic and thermodynamic issues: Given a particular protein sequence, what is the conformation of the folded state? What path does the unfolded chain follow to reach this folded state? This chapter outlines the history of the protein folding problem, current research efforts, the obstacles to accurate prediction of protein structure, and the areas for future inquiries.

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As researchers have pursued biology's secrets to the molecular level, mathematical and computer sciences have played an increasingly important role—in genome mapping, population genetics, and even the controversial search for "Eve," hypothetical mother of the human race.

In this first-ever survey of the partnership between the two fields, leading experts look at how mathematical research and methods have made possible important discoveries in biology.

The volume explores how differential geometry, topology, and differential mechanics have allowed researchers to "wind" and "unwind" DNA's double helix to understand the phenomenon of supercoiling. It explains how mathematical tools are revealing the workings of enzymes and proteins. And it describes how mathematicians are detecting echoes from the origin of life by applying stochastic and statistical theory to the study of DNA sequences.

This informative and motivational book will be of interest to researchers, research administrators, and educators and students in mathematics, computer sciences, and biology.

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