The Department of Biomedicine

BBB Seminar: David A. Case

Biomolecular simulations: implicit solvent models and protein-ligand interactions

Biokjemisk Kollokvium (NBS, Bergen Division)

David A. Case
Department of Chemistry & Chemical Biology and BioMaPS Institute, Rutgers University, Piscataway, NJ, USA

Simulations of biomolecules often use a simplified description of solvation effects, instead of explicitly representing individual solvent molecules. Continuum dielectric models often work well in describing the thermodynamic aspects of aqueous solvation, and approximations to such models that avoid the need to solve the Poisson equation are attractive because of their computational efficiency. I will discuss the generalized Born model, which is simple and fast enough to be used for molecular dynamics simulations of proteins and nucleic acids, illustrating both energetic analysis of protein-ligand interactions and studies of the mechanical and electrostatic properties of linear and circular DNA, and binding of monovalent and divalent ions to nucleic acids.

Host: Knut Teigen, Department of Biomedicine