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Which level does protein structural bioinformatics work at?

1. Quantum level (orbitals and energy bands)
2. Sub-atomic level (charges, electrons, protons, and neutrons)
3. Atomic level (bonds)
4. Molecular level (protein-protein interaction)

Explain with example(s).

As far as I realize, protein bioinformatics works at levels #3 and #4.

At level #3 we have HBond detection algorithms. At level #4 we have secondary structure prediction, protein-protein interactions and binding, etc.

EDIT: I have a CS background, and I am struggling to comprehend bioinformatics as I have no chemistry or biology background.

When I read a protein-related book, it seems to talk about it from either a biological or chemical point of view rather than a mathematical point of view.

I am trying to develop a protein simulation and analysis framework, but I don't know how much detail I should incorporate.