ECompute: Computing the Energy of a Protein Structure

A simple interactive Python program to calculate and compare protein structure energies.

Quick Start Guide

Our main executable file main.py imports the following files: ecalc.py, protein_class.py, dataframefunction.py, and dict_output.py. We used Python 3.7.6 as well as Spyder IDE for development. All outputs are placed in the current working directory.

Protein selection

Protein are selected using R script. R studio will support the Protein.selection.rmd

Clean up

Official pdb clean ups and server-predicted pdb clean ups can be find in clean_up folder

Visualization of protein sturcture

Protein structures are visualized and compared using SwissPdb Viewer.

Reproducing our Results

We requested the conversion of many pdb files to .crd format. All of these files are contained within the zip archive titled "Platform_Analysis_Input" should one wish to replicate our data analysis.

Team

• Tyler Brassel: Built pipeline and main method.
• Xinzhe Li: Managed protein selection and visualization.
• Yinuo Zhang: Performed pdb clean ups and data frame processing.