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PDB Project

PDB

A Java command line tool for fetching protein structures, calculating distances between residues, finding lowest cut-off distances and displaying interaction zones automatically.

GitHub license

This is my final year project of my bioinformatics bachelor degree

INSTRUCTIONS

  • 1. Find all molecular complexes from the Protein Data Bank (PDB), i.e. 2 or more molecules.

  • 2. Calculate the distances between 2 residues of 2 molecules from a PDB molecular complex.

  • 3. Give all the residues within a threshold distance given by the user.

  • 4. Test on 10 given cytokine/cellular receptor complexes. Find out what are the shortest distances and define empirically "interaction zones" between atoms of different molecules. This will define a cutoff distance used below.

  • 5 Define an interaction zone between 2 proteins of a molecular complex i.e. all the residues located at a lower distance than the cutoff one. Apply this to the 10 cytokines complexes and represent all interaction zones by coloring distinctively all the residues located in that zone.

  • 6. Define for a cytokine/receptor complex all the interaction zones containing the nearest residues and color them.

INFO

This tool gather PDB structures by their mmCIF format (key/value dictionary). It parses all useful info for calculating atomic distances (taken from alpha carbons), lowest distances between structures. Interaction zone is a 3D space in which all colored atoms have a distance lower than 8 Angstroms between each entity/polymer (protein-protein/protein-molecule etc.)

USAGE

This is a command line tool launched with the main class App.java A menu of 5 choices is displayed :

  • Fetch all molecular complexes of 2 entities from the PDB API
  • Calculate distances between 2 random residues taken from each molecule of a complex
  • Give all the minimal distances found between atoms of each molecule
  • Choose a structure or a cytokine/receptor complex and display interaction zones with Jmol

RESULT

Example 1

The first protein or entity is in green-ish blue, the second is in yellow and the interaction zone between the two is colored in red.

Example 2

TODO IMPROVEMENTS

  • Add language menu option
  • Add menu in english
  • Clean up info printing on screen
  • Add new feature : more than 2 molecules handled
  • Resolve bug to force ending of program when jmol is launched
  • Add option for calculating distances with CNO atoms
  • Add option to color differently all atoms within their chain
  • Choose a random or chosen structure and display interaction zones

AUTHOR

Karine Dias

LICENCE

MIT