Molecular dynamics and related computational methods with applications to drug discovery

Abstract

The main objective of this review chapter is to give the reader a practical toolbox for applications in quantitative biology and computational drug discovery. The computational technique of molecular dynamics is discussed, with special attention to force fields for protein simulations and methods for the calculation of solvation free energies. Additionally, computational methods aimed at characterizing and identifying ligand binding pockets on protein surfaces are discussed. Practical information about available databases and software of use in drug design and discovery is provided.