I am working on the secondary structure assignment/prediction (actually I am not sure) of proteins using machine learning.
Secondary structure assignment is an automated method that defines the secondary structure (helix, sheet, loop) based on a known three-dimensional structure. Secondary structure prediction refers to taking the primary structure (the sequence of amino acid residues in a protein) and predicting the secondary structure.
There are also some experimental methods that help to characterize secondary structure in the absence of a 3D structure. Circular dichroism spectroscopy gives an estimate of the secondary structure content. Assigned chemical shifts of C-alpha and C-beta atoms from NMR experiments give a residue-by-residue prediction (or characterization) of secondary structure.
What is the difference between structure assignment and structure prediction?
Without the qualifier "secondary", I am unfamiliar with structure assignment. If you google "protein structure assignment", most hits will talk about secondary structure assignment. NMR resonances are assigned to protein primary structure (i.e. which residue gives rise to which signal).
Structure prediction most often refers to tertiary structure prediction. However, you can also predict secondary structure, protein-ligand structures (docking studies) and quaternary structure.
I need a layman's explanation of "protein secondary structure assignment". Adding a diagram or picture would be much appreciated.
Secondary structure refers to the conformation of the main chain in a protein, and the hydrogen bonds between the carbonyl oxygen and the amide hydrogen that are observed. The example below shows that the two secondary structure elements called beta sheet and alpha helix differ in the conformation of the main chain and in their hydrogen bonding pattern.
To assign a secondary structure based on an atomic model, you would measure the main chain torsion angle and deduce hydrogen bonds from distances of hydrogen bond donors and acceptors. Often, the secondary structure assignment is shown juxtaposed with the primary sequence and sometimes with other annotations. Here is an example screen shot. The highlighted Cys30 is part of a helix (red shade) and makes a disulfide bridge with Cys115 (see additional annotation).
Different software packages usually agree on the presence of helices and sheets, but sometime have small differences in the exact start and end of the secondary structure elements (see e.g. here). It is also possible to assign secondary structure from electron density or cryo-EM maps, see e.g. here.