Short Report by Mateusz Sklodowski: Development of a fragment linking algorithm for non-canonical amino acid-based peptide design (June-August 2023)
This summer, I had the incredible opportunity to travel to Nashville as part of my PhD project, collaborating with local scientists. Additionally, my internship coincided with attending the RosettaCon conference in Seattle, renowned for being one of the finest computational structural biology conferences. It boasted a multitude of captivating talks and provided a valuable chance to connect with fellow researchers. This trip also allowed me to participate in Meiler’s Lab retreat held in the breathtaking Great Smoky Mountains.
My PhD research focuses on peptides, specifically designing therapeutic candidates using non-canonical amino acids. In Nashville, my primary goal was to explore the capabilities of existing software for designing peptides based on non-canonical amino acid fragments. Collaborating with Dr. Eric Bell, I conducted several series of screening experiments using a developed pipeline targeting the main protease of the SARS-CoV-2 virus. My time in Nashville not only enabled me to establish a new pipeline for this research problem but also enhanced my coding abilities. It provided an excellent opportunity to learn about my colleagues’ projects and delve into the applications of machine learning in addressing structural biology challenges.
Beyond the scientific aspects, my journey took me to the East Coast of the USA, where I explored Boston, Providence, and New York—specifically chosen as some of the oldest parts of the United States. A highlight was touring several museum ships, notably the USS Constitution, the oldest ship in active service and USS Intrepid,a veteran of the Second World War, having on board one of the space shuttles – the Enterprise. Boston, in particular, left a lasting impression on me due to its historical significance, diverse architecture, and exceptional culinary offerings. During the lab retreat, I embraced outdoor activities, hiking up Mount Le Conte, trying whitewater rafting, and savoring the awe-inspiring views of the Great Smoky Mountains.
I extend my gratitude to the Max Kade Foundation for granting me the opportunity to participate in this program and for making this unforgettable journey possible.