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
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.
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 List
These simulations are housed in a novel relational, multidimensional Dynameomics
Database; see the Database page for more details.
The simulation protocols, software, and analyses are described on the Methods page.
Various methods have been developed to mine, visualize, and analyze the simulations, including our new DIVE:
Data Intensive Visualization Engine for visual analytics; see the Data Mining page
for further details.
As of June 2014, we have performed nearly 20,000 simulations
for a combined simulation time of nearly 800 microseconds. This site currently
contains the native simulations for our Top 100 targets.
If you make use of our website, simulations, or database, please cite our webpage or
previous publications as appropriate. See the Help section