Short Report by Paul Eisenhut: Evolutionary optimization algorithms to explore chemical combinatorial space. (Jan.-March 2022)
Early in 2020 I started my Master Thesis by developing an evolutionary algorithm to optimize small molecules binding to protein targets of pharmaceutical interest. It was planned to start the project at Vanderbilt University in close cooperation with Rocco Moretti, the leading developer of small molecule code in the Rosetta Software suite. He is Assistant Professor in Jens Meilers group at VU. Unfortunately, the Covid pandemic struck, and the trip was canceled. This year, however, I got awarded another opportunity to travel to Vanderbilt for 8 weeks, now a PhD student and the initial project close to being published.
Working closely together with Rocco Moretti and other Meiler lab scientist I was able to refine RosettaEvolutionaryLigands (REvoLd) options system making the software more easily approachable and adaptable to individual user needs. I could introduce it to several people who are deploying the algorithm now to their own research topics. Furthermore, I could install my software on Vanderbilts high performance compute cluster ACCRE allowing even more productive access to it for other researchers. Lastly, I joined a collaborative effort of several lab members to participate in the CACHE competition to design novel bioactive molecules in-silico. It was highly productive exchange providing lots of new experiences and deeper understanding of several technologies to me and allowing me to introduce others to my software solution, adapting it to their needs and making it readily available.
Even though this was my second visit to Nashville, Tennessee, I got a plethora of new insights into southern US culture and society. I spent my nights and weekends diving into the local bar and electronic music scene. I experienced Nashville and its diverse people aside from the touristic and buzzing downtown and Broadway area. This led to many intimate friendships and bonds still existing today. I got invited to celebrate a birthday at a family ranch in rural Tennessee, hiked to one of the many waterfalls in the area, joined plenty traditional BBQs, and many more. This deep dive into southern hospitality is an experience I value tremendously. My experience of the diverse US society was rounded up by a trip to Miami, Florida, including a road trip to Key West.