JED

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.

Please report bugs by submitting a new issue tagged with BUG:
- Be sure to provide enough data to reproduce the error
- Include JED input files, JED errors, and Java stack traces
Please suggest new features by submitting a new issue tagged with NEW FEATURE or ENHANCEMENT
Please contact me if you wish to become a collaborator on this software:

New JavaDocs
New Jars
New Tests
Minor code fixes
- Added FES to JED Driver (now version 1.1)
- Created new input files
- Fixed Pymol script output (now works with educational license)

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