Dynameomics - Protein folds by Molecular Dynamics Simulation

Valerie Daggett and her team at UW have put up a site with their simulations of over 300 proteins for a combined simulation time of more than 35 microseconds. This site contains information for their top 30 targets.  The other interesting part is that they have built this using SQL Server and use SQL Server Analysis Services to create cubes of the molecule locations.


Dynameomics is a continuing project in the Daggett group to characterize the native state dynamics and the folding / unfolding pathway of representatives from all known protein folds by molecular dynamics simulation.

This effort began with the creation of a consensus fold list. This was done by cross-referencing the fold definitions used in SCOP, CATH, and the Dali Domain Dictionary as described in the Origin of the Fold List page. Next, targets were selected from the consensus fold list. A target refers to a specific protein structure from the PDB that has been chosen to represent a given fold (see the example on the left). The specifics of this choice are give on the Target Selection page. The complete list of consensus folds, their populations and targets are provided in the fold and target pages.

At this time, we are continuing to simulate targets from the fold list, generally in order of decreasing fold population. The simulation protocols, software, and analyses are described on the methods page.

Source: Dynameomics - Home Page