Maya Huffman ’22

Rutgers University, New Brunswick, NJ

Writing code that looks at information of proteins based on documents stored on the Protein Data Bank website.

I worked in the Khare lab at the Center for Integrative Proteomics Research at Rutgers University. The Khare lab has both “wet” and “dry” labs, meaning that members of the lab may be doing molecular biology in the wet lab or computational work on protein design in the dry lab. The general process of this lab is to start from protein design using a software called Rosetta (or the affiliated Python library, PyRosetta), and then go into the wet lab to create the designed proteins. Unlike some labs, this lab does not specifically focus on one type of disease, organism, cell line, or even mechanistic pathway. All of the projects are vastly different, but each of them uses the general system of utilizing both protein design and traditional molecular biology.

Before the summer, I had mostly wet lab experience, so I was pleasantly surprised to be assigned a completely computational project and that my project would be implementing a no protein design. Therefore, I functioned much more as a computer scientist than as a chemist or a biologist, though knowledge about metalloproteinase properties was still necessary for my work. The goal of my project was to analyze general trends of the binding sites of proteins containing metal atoms. I did this by writing code that would read through PDB files (documents that contain information about the atoms in a protein), analyze this information, and organize and present this information in a useful way.

Though the work I ended up doing was very different than what I had expected going into the summer, I think that it was an extremely valuable experience. I never thought that I would have the chance to learn how to code, and working in the Khare lab on a computational project has made me very comfortable coding in Python. While coding, I was able to understand my starting point and my final goal, but since I was writing all of the code by hand, I also had to think about every step in between the input and the desired output. I believe that learning Python and writing code will help me think about how to break down big problems into smaller and smaller components. This may be the most useful skill I take away from this summer internship.

I also discovered from talking to the other graduate students and undergrads that the Khare lab is not a very typical research laboratory. Many of the graduate students worked different jobs for several years before deciding to pursue their Ph.Ds. From these graduate students, I learned both about the process of applying to graduate schools, and how important personal motivation is to the entire process. In addition, it was very interesting talking to the undergraduate students from Rutgers University who work in the lab year-round and how that differed from my education at Williams.

Everybody in the lab was very friendly; thus I was made to feel more like co-workers rather than mentee making my summer feel much more fulfilling and productive. I was able to discuss ideas and think with my graduate student mentor rather than simply being told what to do or being ignored while struggling through problems alone.

I believe that experience in coding and experiencing the dynamic of a research laboratory at a big university were two of the most important things I learned over the summer. In addition to this, I also know a bit more about the field of computational biology and about Rosetta labs.

I would like to thank Mr. Chapman and the ’68 Center for Career Exploration for this amazing opportunity; for without them I would have not been able to achieve such skills or to have met such wonderful people that I did over the course of my internship.