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Unformatted text preview: CS 3824 Final Project. Group work. 1 Motivation Proteins are cellular workhorses they perform most of biological functions. Often, protein function includes uptake and release of other small molecules such as oxygen. These enter into the protein via channels or path- ways connected voids in the tightly packed protein structure. Examples of such proteins include hemoglobin that carries oxygen around our bodies, or myoglobin that stores oxygen in muscle cells (it is oxygen-rich myoglobin that makes fresh meet look red). Being able to determine voids and pathways inside proteins is important from both pragmatic (medical) and fundamental (how things work?) reasons. 2 The assignment Design, implement, and test a basic, simple algorithm that searches out for empty cavities in proteins. It does not have to be the most efficient or elegant one. It just has to work. 3 Definitions 3.1 Protein A protein can be uniquely specified by (X,Y,Z) coordinates of its every atom i , see any file from the Protein Data Bank (PDB). Each atom is assumed to be a solid sphere of radius ( x i , y i , z i ). Typically, 1 2 (in atomic length units called Angstroms). Proteins are tightly packed globs of atomic spheres, Fig. 1. Neighboring atom spheres can touch and even overlap. In fact, it is this intuitive and physically sound representation CPK that is utilized by most freely available visualization codes (e.g. textttrasmol ) used to visualize protein structures. For example, carbon atoms are often displayed as a grey spheres, nitrogen are shown as smaller blue spheres. An atom whose name begins with an M would be displayed as a purple or magenta sphere. A typical protein contains between 500 to 3000 atoms. 3.2 Voids and Cavities Figure 1: A typi- cal small protein (myo- globin) in the so-called CPK or space-fill representation. Each atom is shown as a sphere of appropriate radius....
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This note was uploaded on 01/23/2012 for the course CS 3824 taught by Professor Staff during the Fall '08 term at Virginia Tech.
- Fall '08