PDBParser is a computational tool used for parsing and analysing protein structural information from Protein Data Bank (PDB) files. The main purpose of the tool is to analyse the frequency and composition of the two main elements of protein secondary structure, namely alpha-helices and beta-sheets. Currently, PDBParser accepts PDB files containing single and multiple polypeptide chains and a single structural model, i.e. files that do not contain MODEL/ENDMDL tags.
All PDB files used for testing purposes of the script are available as a .zip file in this repository.
- Determines the number of alpha-helices in a protein.
- Computes helixID, length of each helix, and the mean length of a helix.
- Determines the number of beta-sheets in a protein.
- For each sheet, determines the sheetID, number of strands and total number of residues.
- Computes the mean number of strands and residues in a sheet.
- Calculates the number of polypeptide chains in a protein and the length of each chain.
- Computes the overall percentage of residues in a helix, in a sheet and in neither structure.
- Accepts a single PDB file.
- Calculates the frequency of each amino acid in a protein sequence.
- Accepts multiple PDB files.
- Calculates the frequency of each amino acid across all provided files.
- Calculates the residue frequency separately for helical, sheet and irregular segments.
- Computes the propensity of each residue to be in each type of secondary structure.
- Produces barchart plots of the residue distribution in a single protein (4) and the residue propensities (6).
- Python 2 or 3
- matplotlib