1. Formal Model of 3D Protein Structures for Functional Genomics, Comparative Bioinformatics, and Molecular Modeling

Proteins are the main molecules of life. Understanding their structures, functions, mutual interactions, activity in cellular reactions, interactions with drugs, and expression in body cells is a key to efficient medical diagnosis, drug production, and treatment of patients. This chapter shows how proteins can be represented in processes performed in scientific fields, such as functional genomics, comparative bioinformatics, and molecular modeling. The chapter begins with the general definition of protein spatial structure, which can be treated as a base for deriving other forms of representation. The general definition is then referenced to four representation levels of protein structure: primary, secondary, tertiary, and quaternary structures. This is followed by short description of protein geometry. And finally, at the end of the chapter, we will discuss energy features that can be calculated based on the general description of protein structure. The formal model defined in the chapter will be used in the description of the efficient solutions and algorithms presented in the following chapters of the book.