A protein is a sequence over the alphabet of the 20 common amino acids. This is the so-called primary sequence of the protein. For most proteins the primary sequence determines the folded three dimensional structure of the protein – its tertiary structure. In principle it should be possible to predict the tertiary structure from the primary sequence, but we did not know how to do this well in general. And then, in 2018, Deepmind's (google's) 'Alphafold' program handsomely won the 'Casp13' protein structure prediction competition. Subsequent versions got better and better and Demis Hassabis and John Jumper were awarded one half of the 2024 Nobel Prize in Chemistry[1] for this work.

As an intermediate step, the secondary structure of a protein is sometimes considered. This is the collection of relatively "local" parts of the the 3-D structure of the protein. Typically these may be classified as {extended, helix, other}, although finer classifications are also used.

Protei folding is further complicated by the fact that some proteins require other proteins, chaperonins, to assist them to fold, and may be in a local, rather than a global energy minimum, when finally folded. And a protein cannot truly be considered in isolation or at rest – its vibrational energy and the energy due to interactions with other molecules, notably water, may be of the same order of magnitude as the energy due to the protein's fold itself.

Refernces

[1] Nobel Prize in Chemistry, 2024, [www].