Representative Protein Sequence and Structure Database

The database provides the information about the non-redundant protein dataset (1573 proteins) obtained from the Protein Data Bank. The information includes PDB ID, Length of the protein, Resolution, PDB Secondary structure, PDB secondary structure summary, PHD secondary structure prediction, PHD secondary structure prediction summary, sequence. We further revised the PDB Secondary structure summary by reducing the eight state assignments to three states. The database provides additional information about the revised PDB secondary structure summary and revised PHD secondary structure prediction summary, often useful for further improvement of prediction methods. The proteins with unknown 3D structure and function were searched against the RPSSD and found similarity in their secondary structure patterns with the proteins of known structure in our database. This secondary structure information of proteins is furthermore useful in recognizing novel folds in proteins with unknown 3D structure. We are in a process of developing an interactive web interface with the non-redundant protein dataset to enhance the prediction methods and to make this approach as a novel fold recognition method.