I had to break it to you, but you cannot predict protein folding directly from first principles. Nor can any deep-learning model.

You can use molecular dynamics. Maybe, if you are lucky and have the computational resources to do so.

You might want to relate molecular dynamics to "simple rules", but you would be delusional. Molecular dynamics typically use classical forcefields parameterized on data and some quantum simulations. It is not based on first principles.

Proteins fold in patterns generated over millennium of natural selection. It is not simple.