From Sequence to Structure: Fundamentals of Protein Sequence and Structure Analysis
Seoul National University
Please note: this talk will be held in the Ó³»´«Ã½ Auditorium (415 Main St.)
Comparing protein sequences and structures is a cornerstone of computational biology, yet each approach comes with trade-offs in sensitivity and scalability. In this primer, we will begin with the fundamentals of sequence alignment and k-mer–based similarity search, highlighting both their strengths and limitations. We will then turn to structural alignment, introducing methods such as TM-align and motivating the need for alternative representations like 3Di. Building on this, we will briefly discuss Foldseek and how it enables fast structural comparisons at scale. Finally, we will explore the motivation for clustering protein sequences and structures, why it is necessary in large-scale datasets, and the different strategies that can be applied. Through simple illustrative examples, this primer aims to provide participants with the background knowledge needed to understand subsequent discussions on exploring the protein universe with accurate structural predictions.