Algorithms in Structural Molecular Biology (Hardcover)

Using the tools of information technology to understand the molecular machinery of the cell offers both challenges and opportunities to computational scientists. Over the past decade, novel algorithms have been developed both for analyzing biological data and for synthetic biology problems such as protein engineering. This book explains the algorithmic foundations and computational approaches underlying areas of structural biology including NMR (nuclear magnetic resonance); X-ray crystallography; and the design and analysis of proteins, peptides, and small molecules. Each chapter offers a concise overview of important concepts, focusing on a key topic in the field. Four chapters offer a short course in algorithmic and computational issues related to NMR structural biology, giving the reader a useful toolkit with which to approach the fascinating yet thorny computational problems in this area. A recurrent theme is understanding the interplay between biophysical experiments and computational algorithms. The text emphasizes the mathematical foundations of structural biology while maintaining a balance between algorithms and a nuanced understanding of experimental data. Three emerging areas, particularly fertile ground for research students, are highlighted: NMR methodology, design of proteins and other molecules, and the modeling of protein flexibility. The next generation of computational structural biologists will need training in geometric algorithms, provably good approximation algorithms, scientific computation, and an array of techniques for handling noise and uncertainty in combinatorial geometry and computational biophysics. This book is an essential guide for young scientists on their way to research success in this exciting field.

利用資訊科技工具來理解細胞的分子機制，對於計算科學家來說既是挑戰也是機會。在過去的十年中，已經開發出了新的演算法，用於分析生物數據和合成生物學問題，如蛋白質工程。本書解釋了結構生物學領域的演算法基礎和計算方法，包括核磁共振（NMR）、X射線晶體學以及蛋白質、肽和小分子的設計和分析。每一章節都提供了重要概念的簡明概述，重點介紹該領域的一個關鍵主題。其中四章節提供了關於NMR結構生物學相關演算法和計算問題的短期課程，為讀者提供了一個有用的工具包，以應對這個領域中迷人但棘手的計算問題。一個重要的主題是理解生物物理實驗和計算演算法之間的相互作用。本書強調結構生物學的數學基礎，同時在演算法和對實驗數據的細緻理解之間保持平衡。三個新興領域特別適合研究生進行研究，它們是：NMR方法學、蛋白質和其他分子的設計，以及蛋白質靈活性的建模。下一代計算結構生物學家需要接受幾何演算法、可證明良好的近似演算法、科學計算以及處理組合幾何和計算生物物理中的噪聲和不確定性的一系列技術的培訓。本書是年輕科學家在這個激動人心的領域取得研究成功的必備指南。