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Bioinformatics Programming

dssp_parser: A new Python package to extract helices from DSSP files.

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A new Python package named ‘dssp_parser‘ is developed to parse DSSP files. This package fetches all helices including long and short ones from DSSP files.

dssp_parser consists of Python scripts that extract long and short helices in separate files. You have to assign secondary structures using DSSP [1] to the PDB [2] structures from which you want to get helices.

Requirements

This package requires Python3.

Prepare your files

Download the package and save all DSSP files in the ‘dssp_files‘ directory or provide a full path in the scripts if saved elsewhere. Similarly, you can provide the path to your output directories in the scripts.

Usage

$ python3 parse_longH.py

or

$ python3 parse_shortH.py

The program will fetch long and short helices in separate directories. It will name the helix files according to their occurrence in the .dssp file.

Availability

The package is available to download from the GitHub account. The test data is also provided in the given directories.


References

  1. Frishman, D., & Argos, P. (1995). Knowledge‐based protein secondary structure assignment. Proteins: Structure, Function, and Bioinformatics23(4), 566-579.
  2. https://www.rcsb.org

Dr. Muniba is a Bioinformatician based in New Delhi, India. She has completed her PhD in Bioinformatics from South China University of Technology, Guangzhou, China. She has cutting edge knowledge of bioinformatics tools, algorithms, and drug designing. When she is not reading she is found enjoying with the family. Know more about Muniba

Bioinformatics Programming

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Extracting first and last residue from helix file in DSSP format.

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