Computational Biology exam + answers

Test Details The exam will be held on Friday, December 10, 2021 from 3:30 PM PM - 6:30 PM (in 320-105). The exam will be closed-book, but you may consult one double-sided 8.5x11 page (or two single-sided pages). Instructions These are practice questions in the style of questions you might expect on the exam. Each question should be answerable in a few sentences (that is, you’re not required to provide a great deal of detail). Question 1: Compare and contrast the energy functions used for molecular dynamics simulations and those used for ab initio protein structure prediction. Solution: Molecular dynamics simulations use a molecular mechanics force field. This is a potential energy function — it specifies the energy of each precise arrangement of atoms, and therefore allows one to compute the force acting on each atom. The terms in most molecular mechanics force fields are physics-based. Ab initio protein structure prediction generally uses an (approximate) free energy function, which specifies the energy associated with a set of atomic arrangements, and thus allows one to pose protein structure prediction as a minimization problem.