Abstract
Proteases are one of the highest value commercial enzymes as they have broad applications in food, pharmaceutical, detergent, and
dairy industries and serve as vital tools in determination of structure of proteins and polypeptides. Multiple application of these
enzymes stimulated interest to discover them with novel properties and considerable advancement of basic research into these
enzymes. A broad understanding of the active site of the enzyme and of the mechanism of its inactivation is essential for
delineating its structure-function relationship. Primary structure analysis of alkaline protease showed 42% of its content to be alpha
helix making it stable for three dimensional structure modeling. Homology model of alkaline protease has been constructed using
the X-ray structure (3F7O) as a template and swiss model as the workspace. The model was validated by ProSA, SAVES,
PROCHECK, PROSAII and RMSD. The results showed the final refined model is reliable. It has 53% amino acid sequence identity
with the template, 0.24 Å as RMSD and has -7.53 as Z-score, the Ramachandran plot analysis showed that conformations for 83.4 %
of amino acid residues are within the most favored regions and only 0.4% in the disallowed regions.