Software

PhageModifier

PhageModifier is a pipeline of open-source computational tools designed to modify proteins, and in particular phage proteins, to have high affinity for a small molecule. The pipeline is written in Bash, and combines fpocket, PocketAnneal and AutoDock to ensure a seamless experience of protein modification. It comes equipped with a database of crystal structures of phage tail proteins which we have curated, as well as important functional and structural information on their usage.

Our PACMAN project involved lot of time-consuming computational work, and thus we decided to build PhageModifier, which would help users to easily modify proteins leaving the pipeline to take care of the technical stuff in the background.

Dependencies

PocketAnneal requires Python 2.7.12 and reccomends Ubuntu 16.04 for its usage. PhageModifier has been successfully tested on Ubuntu 14, Ubuntu 16 and Elementary OS. These OS are freely available with plenty of help on their usage.

Numpy needs to be downgraded to version 1.8 to run PocketAnneal. This can be done easily with:

>>sudo pip install numpy==1.8

Installation

PhageModifier is available for download at: https://github.com/preetham-v/phagemodifier

The downloaded zipped file can be extracted either the user interface or by entering

>>unzip PhageModifier-master.zip

in the terminal. Once the folder is unzipped, follow the instructions to set up fpocket:

>>cd PhageModifier-master/fpocket-src-1.0
>>make
>>make test
>>make install

Test Run

In order to do a sample run which will help the user familiarize themselves with the software, we have provided two example files, namely example_2xgf.pdb and example_petn.pdb which are our input protein and ligand respectively. Enter the following command in the terminal:

bash pipeline.sh example_2xgf.pdb example_petn.pdb TestRun

The terminal screen will then display the commands being run. Once the pipeline has finished, a new folder called TestRun will be created which contains our created output files.

Persistence

We believe that the act of trying an experiment n number of times without success is very important for it to succeed on the n+1^th try. Every trial adds something new to our knowledge of the experiment and allows for a better execution on the subsequent trial. As such, the numerous failures we encountered on the way were not as disheartening as they would’ve been without this proposition to guide us through. From trying the interlab experiments multiple times only to realise that we weren’t doing the dilutions properly to finding out that our protein is forming inclusion bodies, the number of trials helped us realise mistakes that we hopefully won’t make in the future.

Persistence in work, in spite of the number of failures we faced, paved a way for the team to carry out their work without any major roadblocks.

After iGEM

A team that truly believes in the applicability of their project will realise that there are opportunities even after iGEM that can help take their ideas forward. PhageShift is something we believe can form a base of innovation for building specific and customisable antibiotics in the future. The first step would be to make phages a more acceptable form of medication, something we’ve tried to do with our human practices endeavours. The second step would be to grow out of iGEM and aim for a more in-depth study into phage bacteria interactions that will develop out of our modifications - which cannot be done in the time-frame of a single iGEM competition.