Simbios Talk by Russ Altman, Daniel Herschlag, Vijay Pande, Stanford University, November 8, 2005

Title: RNA DBP

Abstract: The RNA DBP focuses on the folding and dynamics of RNA, particularly  the tetrahymena group I intron.   In this review of progress, we will  touch upon the details of year 1 accomplishments, and suggest the DBP  trajectory for the next year, including new problems.  The areas of  progress include:
1.  Analysis of experimental data to extract kinetic pathway information for RNA
2.  Coarse grain simulations to understand the structural features of kinetic intermediates
3.  Experimental-computational correlation of ion atmosphere studies.
4.  Improving coarse grain sampling power with replica exchange methods

Areas for focus in the coming year:

1.  Test utility of normal mode analysis for RNA dynamics
2.  Test parameterization of coarse-grain potentials, by their ability to generate plausible RNA structures with limited data
3.  Distribute ion atmosphere code as hardened, downloadable application
4.  Distribute coarse-grain RNA modeling code
5.  Create and distribute RNA morphing application at "physics level 0-1"