Applications of computational methods to simulations of proteins dynamics

Abstract

The present advanced state of the computer hardware offers superb opportunities for further explorations of protein structure and dynamics. Sound and well-established theoretical models are successfully used for searching new biochemical phenomena, correlations, and protein properties. In this chapter, the fast-growing field of computer simulations of protein dynamics is panoramically presented. The principles of currently used computational methods are briefly outlined, and representative examples of their recent advanced applications are given. In particular protein folding studies, intrinsically disordered proteins, protein-drug interactions, ligand transport phenomena, ion channel activity, molecular machine mechanics, origins of molecular diseases, and simulations of single-molecule AFM experiments are addressed. Special attention is devoted to emerging methods of enhanced molecular dynamics.