Question

Which of the following is true regarding Protein flexibility?

(a) Methods have been described for the introduction of side-chain flexibility to both protein-ligand and protein-protein docking

(b) Methods have been described for the introduction of side-chain flexibility to protein-ligand   docking only

(c) The Mean Field principle is rarely used in this

(d) Methods have been described for the introduction of side-chain flexibility to protein-protein docking only

I have been asked this question in an interview.

My question is taken from Conformational Flexibility topic in division Predicting the Structure of Protein – Biomolecular Interactions of Bioinformatics

Answer 1

Correct answer is (a) Methods have been described for the introduction of side-chain flexibility to both protein-ligand and protein-protein docking

For explanation: The Mean Field approach is one type of what are called bounded search methods. Others include the Dead-end-elimination theorem and the A* algorithm. These methods use different approaches to find a solution and a detailed discussion is beyond the scope of this chapter. However, they use a multiple copy representation of protein side chains built using a rotamer library.