Computational techniques to study protein dynamics and conformations

Protein dynamics and conformational transitions are essential for most biological functions. They are the necessary link to connect atomic-level structural details with cellular processes ranging from enzymatic catalysis to signaling, solute transport, or synaptic transmission. In this chapter, we review standard atomistic and coarse-grained techniques of increasing complexity to simulate protein motions and conformational transitions. We present the key theoretical foundations and compare how different standard methods explore the conformational landscape in the case of a protein with known intermediates for a simple conformational change. The goal is to provide nonspecialist readers with a broad overview of available approaches that can be used to obtain a basic assessment of protein flexibility.