Even 'topology' is a little confusing to those more familiar with the term from maths.

For the 'CATH' hierarchical classification, the 'Topology' level is something like the organization of secondary structure in an 'Architecture'. This has some relationship to topology in the general sense, but is a narrower definition.

For me, the 'fold' is what happens after 'folding' occurs, but I take the point that it is confusing.

Topology actually makes some sense here in that a very small number of proteins do fold into knots! This was a huge surprise and completely contradicted most predictions. https://en.wikipedia.org/wiki/Knotted_protein

Heh, yes I'm fairly familiar with knotted proteins, and Willie Taylor's work on them.

Strictly speaking most of them are not mathematical knots either, since the ends are not connected. Some have salt bridges, I seem to recall.

knots in the real world (actual, real knots) don't have tied-together ends either. That's not what a knot is. The study of topology in math works on abstract math-knots.

Generally, any non-covalent bonds aren't considered to be topological connections in proteins, although salt bridges can definitely ahve bond energies not far from covalent bonds.

If I recall correctly, the difference between Architecture and Topology in CATH is that the former is independent of connectivity.

> For me, the 'fold' is what happens after 'folding' occurs, but I take the point that it is confusing.

Same here.

The most accurate term would probably be "tertiary structure". Although AlphaTertiaryStructure is a mouthful. They could have named it AlphaTS.

> The most accurate term would probably be "tertiary structure".

There’s an AlphaFold variant that can predict quaternary structure: https://www.biorxiv.org/content/10.1101/2021.10.04.463034v2

> They could have named it AlphaTS.

TS looks more like “transition state” to me.

Ah, good point. TS would be as bad or worse than "Fold" in this context.

DeepMindProteinStructurePredictor or deep_mind_protein_structure_predictor if you don't like camel case

Yup. I've had this discussion repeatedly with the developers of SCOP and the folks who run CASP and they simply will not budge.