[CS582Reading Assignment 2-1]Fast and accurate protein structure search with Foldseek

Ge Liu

Keywords: structure token

Abstract:

**Additional question 1** 3Di tokens are derived from hand-engineered features of raw 3D structures. What experiment would you propose to examine how well 3Di tokens capture actual 3d atomic structures of proteins?
**Additional question 2** What could be missing from the current featurization when deriving 3Di tokens, and what might be the downside of that? How would you test your hypothesis?

Submission Number: 4