Kaila Bennett, Amitoj Chopra, Jesse Johnson, Enricosagullo

Week 18 Progress Report

Kaila Bennett, Amitoj Chopra, Jesse Johnson, EnricoSagullo

Title of Project: Development of Software Package for Determining Protein Titration Properties

Work Completed:

First this week, the calculations were done by hand to give analytical proof of the values we are trying to calculate using our software. Also, we split the remaining work into groups to complete this project by the end of the quarter. One group (Amitoj & Rico) will now try to implement GUI (Graphical User Interface) into the script to make the software more user friendly. The second group (Jesse Kaila) will be working on the interaction energies.
For the GUI, we are using a package for R called TraitR. This package will allow a window to pop up with buttons; it is relatively simple design. By looking at the R forums, TraitR package will be the best because it will allow us to use the GUI function on Windows, Mac, and Linux systems.
The interaction energies are the Columbic interaction energies that use Columbic function in APBS. To do this, we created a matrix for the example protein we are using 1LY2, which is a list of parwise interactions. We calculated these interactions with different dielectric constant because we are unsure of which is the correct one to use. We are trying to calculate Columbic electrostatic potential which is when we neutralize the backbone of the amino acid and charge the side chains.

Future Work:

The next step for the GUI group would be to expand on the creation of the screen to enter values by implementing code that will be able to call for any protein via the internet. Right now our program is only designed to run with 1LY2 but it should be able to use with any protein. The user will enter the protein they wish to calculate apparent pKa for. The script for that should be done within this week.
For the interaction energy group, will use another program pKa tools and look at the script for that program in calculating apparent pKa. Reverse engineer for our program to calculate apparent pKa by using the script from the other program and implement it into ours.

Project Review:

Our project is running smoothly and there have been no delays. We want to be able to compare our calculations to experimental data. As well, we want to compare our calculations to another programs data and see how closely it resembles that. Dr. Morikis, will help us with getting experimental data that is crucial for the accuracy of our program.