Hello Biotweeps! I’m Darwin, a Chemistry PhD student in my final year (*knocks on wood* *prays to the ancient gods*) at Vanderbilt University. I spend my day writing programs for modelling how drug molecules interact with their targets. The goal is to improve our ability to use computers to predict which compounds will bind to a given disease target and the way they will bind. Better computational, or “dry lab”, experiments complement traditional “wet-lab” experiments, which can often be very time consuming.
I work in the lab of Dr. Jens Meiler (http://meilerlab.org) coding mostly for Rosetta (http://rosettacommons.org/), a software package for structural biology modeling. Rosetta is a collaborative project with 40+ research labs around the world actively developing methods for everything from designing catalytic sites of enzymes to predicting binding of HIV antibodies. You may have come across Rosetta in the form of Rosetta@Home, a citizen science distributed computing project, or through FoldIt, a computer game that converts unsolved protein structures into puzzles for players (see https://boinc.bakerlab.org/ and https://fold.it/portal/). You may have also heard about our recent exploration of comet 67P (just kidding, that is completely unrelated).
My research is focused on protein-small molecule docking and virtual screening for Computer-Aided Drug Design applications. Depending on available collaborations, we work on systems ranging from G-Protein Coupled Receptors to Signal Transducer and Activator of Transcription proteins. Part of the job involves making computational tools more accessible to researchers who may be less well-versed in modelling. This usually means making tutorials, web servers, and graphical interfaces. I would love to continue along these lines after graduation and work in scientific software development. I am also interested in researching rare diseases and using modeling to repurpose “failed” compounds to structurally similar targets.
My undergraduate degree is in Chemical Engineering and Biochemistry from the University of California, San Diego. I had a choice between working on hands-on biomaterials research and molecular dynamics modeling of influenza infections. I chose the latter and went down a computational research path. I planned to do more biochemistry in grad school but a few weeks in the cold room and my terrible gel loading skills quickly changed that.
Besides research, I’m interested in science communication and citizen science, particularly for adult education. I also moonlight as a pub quizmaster and connoisseur of “weird” foods. My non-science dream job would be working in sports analytics. Feel free to talk sports, trivia, or odd eats with me (also scotch…yum).
Sadly, there won’t be as many relevant cute animal GIFs over the course of this week, but I promise there will be dancing protein animations instead. I hope to share my love of computer modelling and to learn more about computing applications in your fields. I am also in the process of starting a new outreach effort and would love some input. There may also be a little structure based contest with a nerdy prize. Stay tuned!