In the proposed system, the table format is created for structuring the pdb file.The system is developed in java,Using Stringtokenizer class in java, String tokens are taken for datatype,table,column name, and the query is generated. Using the prepareStatement method which is available in Prepared-statement class,execute-update method which is available in Connection class, the tables are created in the available databases.there is no limit about the atom storage, per chain resides storage. Too large entries can be stored in an effective way using the table format with the appropriate column name and the data type. The internal data structure of a semi-structured database (XML) is a graph rather than a set of tables. This requires new algorithms to be developed for indexing, searching, updates, and other database operations. So In the proposed system, every datum is kept in a structured table format. So the indexing, searching, updates and other database operations are easy.