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  • Alex Rogers

Update #1 from Alex

Alex Rogers is an IMMERSE Fellow part of the Spring 2024 Cohort.

I feel as though I clicked with my mentor, Netonia Marshall, at our first meeting. She told me that I’m asking questions she wishes she could’ve asked herself back then, specifically in considering advanced degrees. These questions dealt with the pursuit of higher education out of an obligation that may not have been adequately thought out. That is, are you pursuing your PhD for the right reason? Can your goals be achieved without it? Netonia and I also talked about the differences between working in academia and industry settings, and how different credentials may drive one to different roles in the workplace. For instance, we distinguished between how a PhD gives the credentials to access a role of experimental design versus how in lower degrees, one may be performing under that person with the PhD. We discussed juggling the roles imposed on us as women, whether we have asked for them or not. Parenthood, becoming older and taking care of your family, all while maintaining a career and being expected to save face during difficult times. 

Setting aside talk of life outside of the work environment, I also met my new hire buddy Jeremy and had a meeting with Steven Albanese. Steven gave me a look into the role of his position as a computational chemist, which is a position I never really thought about. Cheminformatics seems to be a less common field of study as opposed to bioinformatics, but perhaps that may be my bias as somebody who graduated with a degree in bioinformatics. Additionally, I’ve met with several people working in the Enterprise Informatics team. I’ve even been invited to attend the weekly “Dev Skills” meetings where I can sharpen my coding and gain insight as to the role of a software developer. Regarding the online courses offered by Schrödinger, I’ve also completed module 3 of the high-throughput virtual sequencing (HTVS) course. I thought it was really fun to walk through and visit concepts I had not been familiar with back when I used Maestro in school. I’ve also reached module 5 in the intro course and module 2 in the antibody engineering course.

On 02/07/2024, we were introduced to the project we will be working on this fellowship. I was assigned to work on CDK2 with the structural motif of DFG's out conformation. I have begun my research on the protein and collected various studies to learn from. Not only that, I’ve been using Maestro to observe the structural differences between the in-out conformations for myself. It’s one thing to read about the differences and another thing to be able to view the compounds themselves. Using a combination of the 3D and 2D structures, it is easier to visualize how processes like phosphorylation may occur. I’ve attached two structures I downloaded from PDB showing the orientation of the aspartate and phenylalanine between the in and out conformations when using the bound ligand as a focal point.

CDK2 (DFG-in) Ligand Interaction Diagram (PDB ID: 1A9U)

CDK2 (DFG-out) Ligand Interaction Diagram (PDB ID: 5A14)

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