USE OF TSAR AS A NEW TOOL TO ANALYZE THE MOLECULAR-DYNAMICS TRAJECTORIES OF PROTEINS

There is a lack of tools to analyze simulations of protein molecular d ynamics quantitatively. Our aim is to use calmodulin, a prototypical c alcium-binding protein, to describe a strategy and some tools for extr acting relevant information from dynamics calculations. Our main concl usions are as follows: Autocorrelation vectors may be used to represen t a 3D conformation in an n-dimensional space, where n is variable (n less than or equal to 20-30). On such a transformation, classic statis tical tools (PCA, clustering, etc.) may be used to differentiate or ch aracterize dynamics trajectories quantitatively. TSAR, an integrated p ackage used for quantitative structure-activity relationships, is well suited (after minor modifications) for such a purpose. Finally, this type of strategy is able to point out the effects of the solvent scree ning parameters of the Amber software on the dynamics trajectories of calmodulin.