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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.
About the Author
Bruce R. Donald
is William and Sue Gross Professor of Computer Science at Duke University
and Professor of Biochemistry in the Duke University Medical Center. His
laboratory is associated with Duke’s Program in Computational Biology and
Institute for Genome Sciences and Policy.