ABSTRACT
Biomolecular modeling is an active research area in computational biology. It studies the structures and functions of biomolecules by using computer modeling and simulation[Sch03]. Proteins are an important class of biomolecules. They are encoded in genes and produced in cells through genetic translation. Proteins are life supporting (or sometimes, destructing) ingredients (Figure 60.1) and are indispensable for almost all biological processes [Boy99]. In order to understand the diverse biological functions of proteins, the knowledge of the three-dimensional structures of proteins is essential. Several structure determination techniques have been used, including x-ray crystallography, nuclear magnetic resonance spectroscopy (NMR), and homology modeling. They all require intensive mathematical computing, ranging from data analysis to model building [Cre93]. Example proteins: Humans have hundreds of thousands of different proteins (e.g., hemoglobin protein, 1BUW, in blood in 1a) and would not be able to maintain normal life even if short of a single type of protein. On the other hand, with the help of some proteins (e.g., protein, 2PLV, supporting poliovirus in 1b), viruses are able to grow, translate, integrate, and replicate, causing diseases. Some proteins themselves are toxic and even infectious such as the proteins in poisonous plants and in beef causing the Mad Cow Disease (e.g., prion protein, 1I4M-D, in human in 1c). https://s3-euw1-ap-pe-df-pch-content-public-p.s3.eu-west-1.amazonaws.com/9780429138492/cc3be78c-f644-49c2-b40d-db06d778c1a5/content/fig60_1.tif"/>
