Identifying Calcium Binding Sites in Proteins

Identification of the calcium binding sites in proteins is one of the main barriers to understanding the role of calcium in biological systems. Numerous efforts have been devoted to predicting and visualizing calcium binding sites in proteins with high accuracy and speed. Several methods, such as FEATURE, protein seqFEATURE, or MetSite, used statistical approaches for recognizing calcium binding sites based on a variety of physical and chemical features in calcium binding sites and nonsites. To overcome the disadvantages of the above mentioned approaches, this chapter illustrates three methods based on the geometric and other key features of calcium binding sites: GG, GG2.0, and GSVM. It explains datasets, performance measurement, and detailed implementation of these three methods. Experimental results and discussion are finally presented in the chapter.