- 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.
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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
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Please suggest new features by submitting a new issue tagged with NEW FEATURE or ENHANCEMENT
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Please contact me if you wish to become a collaborator on this software:
Charles David: cdavid@carolina.rr.com
- 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)