Molecular Simulation and Systems Biology - Systems Biology: Networks, Models, and Applications - page 94

The Growing Connection Between Modeling and Experiment
An important new trend that will become very strong in the future
is the blending of experimental and modeling approaches. Over the
last two decades, as the capabilities and accuracy of modeling and
simulation have improved, experimental measurement techniques
have also improved. Experiments using atomic force microscopy
and scanning tunneling microscopy are now capable of probing and
resolving atomic dimensions. Time-resolved spectroscopic methods
on proteins and peptides are capable of resolving phenomena that
occur on microsecond time scales. In fact, we are close to entering
an era of nanotechnology where experimental and modeling technolo-
gies can address similar time and length scales. This is certainly no
threat to either field, since experimental and modeling techniques
give very different kinds of information. In fact, the best benefit is
obtained for science if they are used together. Models are more believ-
able when they make predictions that are supported by experiment.
And when they are believable they provide additional useful infor-
mation that cannot be obtained from experiment. Therefore, in the
future one should expect a growing synergy between experiment
and modeling, with modeling being a key tool in the interpretation
of experiments.
Grand Challenge Problems
There is no end of important phenomena that can be addressed with
the realization of some of the improvements mentioned above. Protein
structure prediction, and the understanding of the mechanisms, path-
ways, and kinetics of protein folding and other forms of biological
self-assembly, are still outstanding problems with high technological
and medical relevance.
There are also large-scale simulation challenges, such as RNA fold-
ing and the structure and function of large cellular structures that need
to be understood at the molecular level. These include the ribosome,
the molecular factory used by the cell to build proteins, and the proteo-
some, the molecular factory used by the cell to degrade them. Large-scale
simulations could advance our understanding of the role and function
of chaperones, proteins that aid in the folding of other proteins. Other
frontiers include the simulation of protein-ligand and protein-protein
interactions, and the detailed modeling of the functioning of membrane-
bound proteins.
ACKNOWLEDGMENTS
The authors would like to acknowledge Frank Suits, Mike Pitman, and
Alexander Balaeff for help with the figures in this chapter.