Modeling biomolecules: larger scales, longer durations

Abstract

The molecules of life are big, complex, and dynamic. Collaborating in multidisciplinary groups that draw on chemistry, physics, mathematics, and other fields, computational scientists are beginning to simulate systems of large biomolecules interacting in time. Obstacles are formidable; the potential benefit, vast. The fast growth of molecular modeling as a research tool in biology and medicine has been tightly coupled to the advent of the supercomputer and to advances in applied and computational mathematics over the past decade. Three features characterize the progress made to date: bigger molecular systems described in atomic detail, longer simulation time scales, and more realistic representations of interatomic forces. With these improvements, molecular modeling by computer has given us many insights into the relationship between structure and function of biopolymers and drugs. Researchers now find it indispensable for structure refinement. Still, the state of the art in molecular modeling leaves much room for more progress.