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Welcome to the JED wiki!

Summary

JED is a powerful tool for examining the dynamics of proteins from trajectories derived from MD or Geometric simulations or NMA. Currently, there are two types of PCA: distance-pair and Cartesian, and three models: Cov, Corr, and PCORR. The idea behind the development of JED was to not only analyze a trajectory, but also compare it to other dynamical analyses. To do this, JED uses subspace analysis to assess the similarity of essential vector spaces defined by each dynamical method. Additionally, JED computes the Free Energy of a trajectory from two PCs (weighted DVPs) so that a FE surface can be constructed. Finally, JED produces PDB frames and script files for viewing movies in PyMol(TM) of both individual modes and a superposition of Essential Modes (default = 5).

Usage

The JED package contains the source code, a set of executable jar files, a set of input files, documentation including the JED paper, the JED Manual, and Supplementary Materials, JavaDocs for the code, a Jupyter Notebook that contains examples of how to run the different drivers, and a copy of the GNU license.

1. Please read the JED paper and Manual
2. Create your input files by editing the ones provided
3. Look at the JED_Testing.ipynb Jupyter Notebook for working examples
4. If you find bugs, please report them by creating an issue tagged with BUG and providing all relevant details including your input file, JED errors, and Stack Traces.
5. Please share your use of JED here... We love to hear about what you are doing with the software.
6. If you would like to request and enhancement or new feature, please submit an issue describing your idea and tag appropriately.
7. Please share your thoughts and experiences with JED on this wiki!