PDB Project

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

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

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.

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