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JED is a program for performing Essential Dynamics of protein trajectories written in Java. JED is a powerful tool for examining the dynamics of proteins from trajectories derived from MD or Geometric simulations. Currently, there are two types of PCA: distance-pair and Cartesian, and three models: COV, CORR, and PCORR.

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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)

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JED is a program for performing Essential Dynamics of protein trajectories written in Java. JED is a powerful tool for examining the dynamics of proteins from trajectories derived from MD or Geometric simulations. Currently, there are two types of PCA: distance-pair and Cartesian, and three models: COV, CORR, and PCORR.

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