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.

Thank you for using JED software:

• 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:

Charles David: cdavid@carolina.rr.com

Last Update: May 2018

• 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)