Home » VR-REU 2024 » Utilizing VMD to Visualize and Analyze Two PDB Files of FNDC1

Utilizing VMD to Visualize and Analyze Two PDB Files of FNDC1

Asmita Deb

Week 1

This week we first started by bowling and getting to know everybody that we would be working with for the next 8 weeks. It was a great team bonding experience and by Monday, when we stepped into Hunter College, everything went smoothly! We went up to a conference room and met with the mentors of everyone in the REU and then we took a tour of the college itself. We came back up and were told our tasks for the week and then left. The next few days were dedicated to creating a proposal for our project that would satisfy our mentor, Dr. Wole, and ourselves. On Wednesday we submitted and discussed our drafted proposals and then finalized them to be submitted on Overleaf. Throughout this we also watched many lecture videos that introduced us to VR/AR and the research tools we would be using. The project that I am planning on focusing on is the utilization of Paraview, a scientific visualization software, to analyze and visualize a protein called FNDC1 whose overexpression is associated with multiple cancers.

Week 2

This week I worked on my literature review. I found about 4-5 sources about the protein, FNDC1, and also using visualization software and how it could benefit the research of understudied proteins. This was the first time I used OverLeaf, but it was easy to get the hang of. I also played around with Paraview all week and downloaded both of my files. I’ve been editing them, but I will be also trying VMD next week, just to see the differences. I also figured out what type of user study I wanted to conduct and what I wanted to specifically write about in my paper. Throughout the week I also enjoyed good food, fun activities, and bonding with the other interns!

Week 3

This week was more focused on the methodology and moving forward in our projects. I inserted both of my PDB files of the two different structures into VMD, but for a lot of the analysis tools in VMD, it is necessary to have some sort of trajectory or movement file. To gain this, I had to download a separate program called GROMACS which is used for a lot of trajectory and molecular dynamics. I didn’t have a lot of previous experience with Homebrew, CMake, or terminal coding, but through this experience I learned a lot. I got my movement files and will now load it onto my VMD protein frames. I have also been working on my research paper on OverLeaf and also watching the videos of the class.

gk protein

Week 4

This week I worked on my midterm presentation that we would be showing to our peers and also the other mentors. The presentation included an introduction to our project, why we were conducting this research, our literature review (papers and works that are related to our project and have significance to our research), our methodology, future work, and a video that served as a demo to what we’ve been doing so far. It was a very stress-free presentation and was used for feedback and help in our projects. In the next week I hope to garner all my data so that I may start working on my survey and send it out by Week 6’s beginning to then start collecting survey data to include in my paper.

Week 5

This week I noted down all of the data that I have accumulated between the two PDB files. I have also started narrowing down the five questions I want to ask for my survey for each protein model, which means I will have 10 questions total. I have started writing down my comparisons and similarities about the two files in a way that is presentable in a research paper. I have been updating OverLeaf as well to keep up with the progress I’m making. My hope is by the beginning of Week 7 I will send out the survey and continue to edit my paper while I await my responses. This would mean that Week 7+8 I am just adding my survey data and finishing up my paper (fingers crossed). It was also 4th of July this week, so it was an odd week, but very fun!

Week 6


This week, I asked my friend to act as my guinea pig with my first and very preliminary survey. The feedback I got was to not ask so many quantitative questions and more so about comfortability with the software as not everyone has a biology background. It is easier to ask if they are able to use the video in my survey to answer the questions than judge if they answered correctly. I have been updating OverLeaf, blog posts (trying to figure out the images). I am going to send out the survey this week and start analyzing my data as it comes in. For fun this week, my best friend from home came to visit and we spent a great time together exploring the city as it is her first time!

Week 7

Wow! We are hitting the last week of this internship and I feel so many emotions. I feel happy, scared, and excited for the future. This week I focused on finalizing the data and information I wanted to include in my paper and what I wanted to really write about as a conclusion of my research. I also finished up my survey this week, sending it to Dr. Wole for a quick run-through and then sending out the survey to everyone and anyone to get the max participants I could. As I wait for more results, I will just start to finish up my paper in OverLeaf and discuss the results I’ve gained so far, as there seems to be a trend. I’ve attached an image below of the trend I’m seeing. For fun, my best friend from college visited this weekend and we had a really great time, also with some of my co-interns as we celebrated our last weekend in NYC!

Hunter College
City University of New York
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New York, NY 10065

Telephone: +1 (212) 396-6837
Email: oo700 at hunter dot cuny dot edu

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