Does that imply proteins have some dynamics that need to be predicted too? I remember seeing animations of molecular machines that appeared to be "walking" inside the body - are those proteins or more complex structures?
A classic example is haemoglobin, that 'just' binds to oxygen at the iron in the middle of the haem. Other binding sites remote from the oxygen binding one can bind to other molecules - notably carbon dioxide. The 'Bohr effect' mechanism is outlined here : https://en.wikipedia.org/wiki/Bohr_effect#Allosteric_interac...
Even at the lowest level, there is some evidence that ligand binding can affect the structure of the backbone of the protein. For example, peptide plane flipping https://en.wikipedia.org/wiki/Peptide_plane_flipping although I'm not sure where the research is on this nowadays.
I think AlphaFold gives us more of a static picture that doesn't tell us much about how the protein will interact with the world. Predicting these dynamic aspects, protein-to-protein interactions, and ultimately an entire cell, is probably what they'll like to do next.
I don't know if the walking buddy is a single protein, it may be a handful of different ones joined together.
I often recommend the book 'Cats' Paws and Catapults' by Steven Vogel, which discusses the differences between human and biological engineering. There are very different constraints, as well as the more obvious difference between intelligently directed design (by humans) and evolutionary design.
It's not totally true that our engineering is simpler than biological systems. After all, we can now manipulate matter down to the atomic level. There have been attempts to move towards self-assembling systems, or even self-repairing ones. Not quite on the same scale or sophistication as biological systems, of course.
Is a modern computer chip more complex than a virus? Is a large connected system of computers more complex than a mycelial network? Are there more parts connected in more ways in a nuclear power station as there are in a simple bacterial cell?
I think it is definitely worth considering the similarities and differences.
I think my sense that biology is more complex than human engineering is that our engineering seems much more homogeneous. Computer chips are certainly very dense but the individual number of different component types are very small. Biology on the other hand seems to have a huge number of fundamental building blocks, e.g. proteins, with different behaviors. I suppose that maybe that's the wrong comparison though and software is where our engineering diversity is present.
It may well just be the case that my lack of familiarity with biology makes it seem more complex to me.
But nobody will ever understand everything about a natural cell. Levels are an ad hoc phenomenon adhered to in varying degrees in certain places to contain variation. But few elements have only one role at one identifiable level, and you can never be sure one doesn't have another. And huge amounts of apparatus might radically change behavior in a subtly different environment.
Software is where the diversity is, for computers. A cells systems are a set of interlocking networks of DNA, RNA, protein, small molecules, and signalling. As you say, these diverse parts then interact in diverse ways.
Another aspect is the large number of 'levels' in biological systems - humans have around seven; atoms, molecules, organelles, cells, tissues, organs, whole system. The interactions within and between these levels is a further source of complexity.
They are called motor proteins because they convert chemical energy into kinetic energy. In the case of kinesin, it forms a dimer (two copies of itself bind together to form the two "legs") and also binds to light chains (accessory proteins that modulate its behavior) so that it can walk along filaments and drag cargo around your cells. They are both proteins and more complex structures because multiple proteins are interacting, as well as binding small molecules and catalyzing them into chemical products, all to produce the motion.
One of my favorite quotes about biology goes something like:
"An alien spaceship lands in your yard. You are kindly invited in to study and tour the ship. The technology is clearly billions of years more advanced than our own. Not decades more, not millennia more, not megayears more, but clearly gigayears more.
This is biology"
Sorry, can't find the exact quote and citation right now!