/PySupercharge

the supercharging library for bioinformatics

Primary LanguagePythonGNU General Public License v3.0GPL-3.0

PySupercharge ⚡🧬

The supercharging library for bioinformatics.

Official Implementation of Supercharge and Secretion paper(Ahn et al.). Official Web Implementation: WebSupercharging

What is PySupercharge? - short introduction -

Decreasing electric charge by modifying amino acid sequence can improve the secretion ability of protein through bacterial ABC transporter system. PySupercharge replaces positive amino acids (Lys, Arg) that satisfy two conditions (AvNAPSA and consurf score) with negative amino acids (Glu, Asp) when the amino acid sequence has a high electric charge locally.

AvNAPSA score

The lower AvNAPSA score means fewer neighboring atoms and therefore less interaction. It ensures that the amino acid replacement will not make a significant change in the shape of the protein.An AvNAPSA cutoff of <150 has been widely used.

Consurf score

Consurf score identifies conserved regions of the polypeptide by tracing evolutionary history. Therefore it can determine whether the amino acid replacement causes functional problems of protein. A consurf score should be less or equal to 5 to be replaced.

Requirements

Python Environment: 3.x. Python Package Dependency: install the requirements.txt file with

python -m pip install -r requirements.txt

How to run

Supercharge analysis

make sure that the requirements are met, and the PyAvNAPSA folder is inside the python\Lib\site-packages Run the follow command in the directory to open GUI interface for the script

python superUI.py

PyMol plugins

  1. install within pymol directory: schrodinger\PyMol2\Lib\site-packages
  2. load the Show_AvNAPSA_Script on PyMol's plugin manager.
  3. Choose pdb/pse model to be loaded.
  4. Adjust threshold cut-off value (default: 80)
  5. AvNAPSA selection is shown in red.

Examples

Supercharging

Inside the example folder, there is a pdb file and a consurf grade file for the 2013PEDV. follow the steps to get the following result:

  1. Import Consurf, sequence should be automatically added after choosing the file.
  2. Import PDB, AvNAPSA value will be calculated in the terminal and might takes a while.
  3. Adjust the threshold (in this case: 3)
  4. Press Supercharge and Export.
  5. The file should be in the same folder as the terminal current directory.
  6. The exported result named result.html should looks like this.

GUI helpful schematic

Contributions

Hieu - superUI, AvNAPSA_class, PyMol plugin.

Hyunjong Byun - AvNAPSA_class, AvNAPSA_dict.

Yerin Kim