If you’ve ever run a molecular dynamics (MD) simulation, you know the feeling. You spend days, weeks, or even months of precious compute time watching your favourite molecule wiggle and jiggle. The result? A trajectory file bursting with thousands, or even millions, of frames. It’s a treasure trove of data, but it’s also a monster…

Analyzing every single frame is often impossible and, let’s be honest, usually pointless. Many adjacent frames are nearly identical. What we really want are the key representative structures that capture the important shapes, or conformations, your molecule adopted. So, how do we find them?