Comment by bckr

> Are people just browsing these shapes and seeing patterns in them

That's one approach.

The thing to understand is that proteins form "binding sites": areas that are more likely to attract other particular regions of proteins or other molecules, or even atoms. Think about hemoglobin. The reason it holds onto oxygen atoms is because it has binding sites.

Binding sites are great because they represent more freedom to do things than molecules typically have. Normal chemistry consists of forming strong electronic bonds between atoms, or forming rigid lattices/crystals.

Binding sites allow molecules to do things like temporarily attach to each other and let each other go under certain circumstances, for instance when another binding site is active/inactive. This can happen through "conformation change", where a molecule bound/unbound on some binding site makes the protein change shape slightly. This is how proteins can act like machines.

> What do the "ribbons" signify

Different regions of the protein have different sequences of amino acids. Amino Acids have somewhat different shapes from each other. The ribbons are actually broader than the spindles (or threads), and less flexible. Not sure about the different colors, maybe someone else can fill in.

> Also, is that what proteins would really look like if you could see at sub-optical wavelength resolutions?

Not really, it's an abstraction. They're big molecules, so if you look closely they're made of atoms, which are (kinda, sorta not really, quantum stuff) spherical.

> So wouldn't they be "thrashing around" like rag doll in blender at room temperature?

Yes, but the attractions between the different parts of the molecule keeps it somewhat under control. So more like an undulating little creature, jellyfish perhaps.

> It seems strange to me that something like that could be so central to life

Yep, gotta remember that it's all statistical. These things are getting made, do their job, breaking, and getting degraded some insane number of times per second. Swarm behavior, sort of.