Continuum Solvent models to study the structure and dynamics of nucleic acids and complexes with ligands

Abstract

The aqueous environment has an important influence on the structure and function of nucleic acids. The explicit inclusion of many solvent molecules and ions during simulation studies on nucleic acids can lead to prohibitively expensive computational demands and limits the maximum simulation time. Many applications such as systematic conformational searches and ligandreceptor docking approaches used for example in drug design efforts require computationally rapid implicit treatment of solvation. Ideally, such implicit continuum solvation models should still be accurate enough to be useful for a realistic evaluation of generated structures or docked complexes. An overview is given on recent developments concerning continuum solvent modeling of nucleic acids and complexes with ligands. This includes applications of Poisson-Boltzmann based as well as Generalized Born type continuum solvent models. A number of studies indicate that conformational search procedures based on continuum solvent models could be useful for structure prediction of nucleic acid motifs and during ligand-nucleic acid docking studies. Shortcomings of continuum solvent modeling approaches as well as possible future improvements are also discussed. © 2006 Springer.