Table 8.

Types of searching applications

Application I: searching a database of complete protein structures with a binding site	Application II: searching a database of binding sites with a binding site	Application III: searching a database of binding sites with a complete protein structure
A. Advantages
1. Can recognize new regions that can function as binding sites	1. Reduced run time and storage space	1. Can be used to recognize an unknown binding site of a protein of interest
2. The database structures can be unbound. No information is missed	2. Less false positives, since we compare only known binding sites
3. All of the solutions are relevant, due to their similarity to a specific region of interest
B. Disadvantages
1. The binding site of a protein of interest must be known	1. The binding site of a protein of interest must be known	1. Large amount of information may be missed
2. Some solutions may align regions which are not binding sites	2. Large amount of information may be missed	2. The query is not focused. Some solutions may align regions which are not binding sites
		3. Development of a reliable ranking scheme is not straightforward

Advantages and disadvantages of three types of applications for recognition of functional sites.