Protein structure prediction is one of the most central areas pursued by bioinformatics and theoretical chemistry. These predictions are very important in drug design and to design of novel enzymes. Many conformational changes takes place in a polypeptide that are responsible for differences in the three dimensional structure of proteins. There are many software to predict the structure of protein, protein threading, homology modeling, secondary structure prediction, ab initio methods, signal peptide prediction and transmembrane helix.