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TRANSMEMBRANE PROTEIN DETECTION

This python program identifies transmembrane regions of proteins, some of its features include:

  • Detecting if a protein is globular or transmembrane.
  • Finding the orientation of the protein in a membrane.
  • Indicating the position of the lipid bi-layer.

Development environment

This program was developped by python 3.9.5.

Conda is needed in order to set up the environment. For conda installation please check the user manual https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html
Run the following commands to create environment:

$ conda env create -f TMDET.yml 
$ conda activate TMDET

To calculate secondary structure and accessibility, you need to download DSSP (see https://swift.cmbi.umcn.nl/gv/dssp/)
To install DSSP on Linux run the following command:

$ conda activate TMDET
$ sudo apt-get install dssp

Usage

  • required arguments:
    -i I input file (pdb)
    -id ID pdb id
  • optional arguments:
    -h, --help show this help message and exit
    -pt PT number of points in fibonnaci sphere (default=100) -o O output pdb file (protein + bi-layer position) run in terminal (example):
$ python3 main.py -id 1XYZ 
$ python3 main.py -i 1XYZ.pdb -o output.pdb
  • Example files for 1uaz proteins are given as part of the package.
  • The output pdb files that include bi layer position can be visualized with appropriate programs such as pymol.

Authors

  • Sabrina SAFAR-REMALI
  • Yanyuan ZHANG

References

  • This work was inspired by the algorithm described in the following article:
  • Tusnády GE, Dosztányi Z, Simon I. Transmembrane proteins in the Protein Data Bank: identification and classification. Bioinformatics. 2004 Nov 22;20(17):2964-72. doi: 10.1093/bioinformatics/bth340. Epub 2004 Jun 4. PMID: 15180935.

GitLab repository

You can find our source code repository and demo files on GitLab at https://gitlab.com/sab.s/python2_project.