Molecular Modeling and Simulation of G-Quadruplexes and Quadruplex-Ligand Complexes

Methods for the molecular modeling and simulation of G-quadruplex structures and their drug/ligand complexes are discussed, and a range of protocols is presented for undertaking a variety of tasks including model-building, ligand docking, dynamics simulation, continuum solvent modeling, energetic calculations, principal component analysis, and quantum chemical computations. The scope and limitations of these approaches are discussed.