Detailed structural analysis of proteins necessitates investigation at primary, secondary and tertiary levels, respectively. Protein Data Bank (PDB) is an internationally referred protein structure database,it comprise of the atomic coordinates of the threedimensional (3D) structures of proteins that are solved experimentally, and as well theoretically. Molecular visualization tools such as RASMOL, PyMOL etc., help to visualize the coordinates of the PDB file in a 3D form, the information pertaining to the fold class, the arrangement of secondary structural elements can also be easily inferred. Pertaining to secondary structural analysis, dissection of a given protein structure into its secondary structural elements is carried out with a view to understand the types of secondary structures involved (apha helices, beta sheets), the number and length of the respective elements, and the amino acid sequence that encode for the secondary structural regions. Of the above, knowing the amino acid sequence of apha helix and beta sheets from the PDB file will help in assessing the relative composition of the different secondary structural elements in a given protein structure or between structures. At present, this can be achieved by manually decoding the coordinate file based on identifiers that are associated with the secondary structural features. Towards an automated extraction of the amino acid sequence corresponding to the secondary structural regions, we developed a standalone tool entitled “Exser”. Exser extracts the amino acids that encode the secondary structural regions of protein structure from a given PDB file. The output will provide the user with the amino acid of the alpha helices and beta sheets that occur in the protein structure. Besides, it also extracts the amino acid sequence of the complete structure.
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