Week 2

I finished my rough pipeline! I finally got to write some code, and managed to write a suite of python functions that helps to query the PDB database, read in the chemical genomic data, and convert all of the molecules and dock them. I’ve learned a lot of python, linux, as well as some biology and bioinformatics. I also went to a symposium on preventative medicine which was interesting both for the new and interesting pharmaceutical/computational science and for experiencing my first symposium!

Now I have to find a better control to test my pipeline, which is proving to be surprisingly challenging because of the limited amount of known protein/ligand complexes with well documented binding structures. The ones they do have are mostly human drugs/proteins, which make it difficult to find ones that are yeast specific. I wish someone just gave me a protein ID and a ligand structure and told me these are perfect matches and this is how they bind. Oh well, I guess that’s just the nature of research.

As for non-project stuff, I’ve also learned Github and LaTex through the training workshops which are useful tools. Yesterday, our lab had a “happy lab hour” which consisted of going to a university saloon and eating apps and talking. It was nice hanging out with the group and hearing more about them outside of their work. Right now, I am currently writing this in downtown Minneapolis! My first time going in, and of course the light rail is under construction, but I managed to take the shuttle and make it out here. A few of the other dreu students and I are going to try to go to a festival, but it’s kind of rainy so I’m not sure how this will work out. We’re also having a comp sci REU tennis tournament later, which will be super fun, and luckily the university loans rackets for free. I’m still amazed by all of the amenities a huge university has.