Protein visualisation and prediction

Web application to visualise protein prediction and proteins in a 3-dimensional space.

Motivation

This project is part of the software engineering course ("GLOG") of the Master of Bioinformatics of the University of Bordeaux. The goal is to provide a web application, dedicated to biologists participating in the "Les Sentinelles du Climat" project, in order to provide visualization and interaction tools with data extracted from protein information of "Les Sentinelles du Climat" species.

Access

The application is available at : https://glog-project.herokuapp.com.

Usage

The user has the possibility to visualize a number of proteins. By clicking on the desired protein, the 3D visualization is displayed in the black frame. The 2D prediction is observable below. Informationw about the protein are presents at the top right. It is also possible to display the 3 proteins ids having their sequence close to the studied protein. Links to the RCSB PDB database for this 3 proteins are available. There is also the possibility of obtaining the Ramachandran diagram of the protein.

Deployement

The application is deployed with Heroku.

Repository import

git clone https://github.com/mablt/GLOG-Project.git

Dependencies

The following dependencies are required for execution :

• flask 0.12.2
• requests 2.22.0
• biopython 1.78
• biotite 0.24.0
• matplotlib 3.1.2
• RamachanDraw 0.2.2
• pypdb 2.0

Authors and contacts

Students of the Bioinformatics Master of the University of Bordeaux.

Marine ALVES DE BARROS - marine.alves-de-barros@etu.u-bordeaux.fr
Mathieu BOLTEAU - mathieu.bolteau1@gmail.com
Mélanie CARRIAT - melanie.carriat@etu.u-bordeaux.fr
Alexandre CORNIER - alexandre.cornier@etu.u-bordeaux.fr Martin DRANCÉ - martin.drance@etu.u-bordeaux.fr Rémy JELIN - remy.jelin@etu.u-bordeaux.fr Abdelghani NEUHAUS - abdelghani.neuhauw@etu.u-bordeaux.fr