Proteases are one of the highest value commercial enzymes as they have broad applications in food, pharmaceutical, detergent, anddairy industries and serve as vital tools in determination of structure of proteins and polypeptides. Multiple application of theseenzymes stimulated interest to discover them with novel properties and considerable advancement of basic research into theseenzymes. A broad understanding of the active site of the enzyme and of the mechanism of its inactivation is essential fordelineating its structure-function relationship. Primary structure analysis of alkaline protease showed 42% of its content to be alphahelix making it stable for three dimensional structure modeling. Homology model of alkaline protease has been constructed usingthe 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 identitywith 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.
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