This week was full of doing tests, further automating the pipeline, and getting some results. There’s still a struggle finding compounds whose known target’s structure has been experimentally validated, but it seems like the pipeline has some merit in finding the right protein depending on many factors that still need to be optimized. As my mentor put it, there is also a lot of information in the different trials. For example, if all of the trials are returning the same exact number for the binding energy than that is local minimum, and the hope is that if it finds a very strong binding energy that is hopefully the absolute minimum. (Remember the minimum energy indicates the correct binding pose of the drug in the protein). Overall, the preliminary results were exciting and the process of coding and running has been a fun (and only a little frustrating) challenge. These results were based on three compounds and three trials of ~10 proteins each. The goal for this week will be running maybe 10 or more trials for each compound and try to validate 10-15 compounds if we can find enough compounds with enough verified information. Updates to come!
As far as outside of research goes, this week has actually been pretty packed with activity! I’ve been going biking along the Mississippi a lot—the biking trails around here are great, as well as the views! Additionally, I am going to the Mall of America for the first time tonight, a Twins game tomorrow, and a concert at the Varsity Theater on Thursday. I’m really glad that DREU assigned me somewhere outside of the Northeast, it is great to experience and explore a different area.