28COMPARATIVE MODELLING OF SER/THR KINASE DOMAIN OF WALL ASSOCIATED KINASE IN Oryza sativa L.This paper shows how homology modeling works for given protein sequence and how it is implemented in Crop Modeling. Homology modeling involves taking a known sequence with an unknown structure and mapping against a known structure of one or several similar protein. The quality of homology modeling is dependent on the quality of the sequence alignment and template structure. Based on this modeling, the unknown protein sequence can be predicted based on the relevance match found from the database. This homology modeling is very useful for molecular docking process. The wallassociated kinase (WAK) proteins have been widely analyzed in plants. They play an important role in seed maturation and osmotic stress. WAK proteins in seeds are related to desiccation tolerance. Among the 5 groups of WAK protein, Group-4 WAK protein of Arabidopsis thaliana is identified for the computational analysis. The homology modeling of the putative protein was generated by using the Modeller software. From 5 models generated from modeler, the final model is selected after analyzing and validating the structure by using the validation server WHAT IF interface. The model is further optimized by performing Energy minimization technique (Steepest Descent)vikramthau@yahoo.co.inResearch322013WAK proteins,Arabidopsis thaliana,Homology modeling,validationVikram SiddarthaG,P.SrinivasanNew villangudi, Madurai, Tamilnadu, India,New villangudi, Madurai, Tamilnadu, India