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SEARCH AND SAMPLING IN STRUCTURAL BIOINFORMATICS
The road was still paved with yellow brick, but these were much covered by dried branches and dead leaves from the trees, and the walking was not all good.
L. Frank Baum, in The Wonderful Wizard of Oz, 1900.
INTRODUCTION
Search and Sampling—Tools of Structural Bioinformaticians
Structural bioinformatics aims to gain knowledge about biological macromolecules utilizing computational methods applied to structural and structure-related data (see definition in Chapter 1). Search and sampling methods aim at providing a focused “yellow brick road” toward understanding the properties of complex biomolecular structures. Such methods must often be tailored for this unique field. First, intrinsic to the “bio” nature of the data is high complexity in the number and the type of variables. Structural data is derived experimentally from various sources and is presented in different resolutions (Chapters 2-6). Moreover, other types of data often need to be integrated in the processing of structural data. These include (1) the exponentially growing sequence data, for example, in the form of evolutionary conservation (Chapters 17, 23, 26), as well as (2) biophysical data, for example, stability of proteins, distance restraints between residues as derived from mass spectroscopy (Chapter 7) or analysis of mutational data. Second, the required representative space (defined later in the chapter) one wishes to study is often biased, not ...
