In this study, robust biological filters are used to combine the datasets for drug discovery. The two protein datasets are combined into a single form using a filtering instance to identify the proper classification algorithm for protein analysis. Big data paves the way for identification of better protein classification algorithm to avoid congestion in the analysis of large volume of data and to save time for the successful results. BLAST algorithm used for the conversion of unstructured protein into a structured protein. The structured proteins in n numbers can be performed with the proposed system model for analysis. Due to this analysis, it helps in identifying new drug target in the biological research with better classification algorithm and also in large class of applications such as next generation technologies, big data mining, protein mining etc. © 2017, Institute of Advanced Scientific Research, Inc. All rights reserved.