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JEDi: Java Essential Dynamics Inspector

JEDi RELEASE NOTES: JEDi is the updated version of JED

Beta Testing Completed
Now in release 1.0
  • JEDi is a powerful tool for inspecting the dynamics of proteins from trajectories derived from MD or Geometric simulations, or NMA.
  • All JEDi features are controlled via an input file containing a list of KEY=VALUE pairs
  • There are 5 Levels of Coarse-Graining:
    • All-Atom by residue
    • Heavy-Atom by residue
    • Back-Bone by residue
    • Alpha-Carbon by residue
    • Atom List
  • There are 4 Types of PCA:
    • Hierarchical Cartesian
    • Direct Cartesian
    • Distance-Pair
    • Residue Pair Interaction
  • There are 3 PCA Models:
    • Covariance
    • Correlation
    • Partial-Correlation
  • There is the option to perform Outlier Processing:
    • Outliers Removal is perfomed at a specified cutoff
    • Outliers Selection is perfomed at a specified cutoff
    • The results of outlier removal and selection are compared
  • There is the option to perform Sparsification of the Correlation and Partial Correlation Matrices:
    • Separate cutoffs are provided for each matrix
    • When both Correlation and Partial Correlation models are selected, an adjacency matrix is provided to help identify activator and suppressor variables
    • The results of sparse and non-sparse analyses are compared
  • All JEDi output is provided as high quality PNG images for immediate inspection:
    • PCs and DVPs
    • Square Modes
    • Scree Plots
    • Variable statistics
    • MSA scores
    • Eigenvector Collectivity
    • Iterated RMSIPs with comparison to random and with Z-scores for significance
  • Kernel PCA post-processing of the reduced data is available, using an assortment of kernels including:
    • Mutual Information
    • Neural-Net (Tanh)
    • Gaussian
    • Log
    • Circular
    • Mahalanobis
    • Euclidean
    • Polynomial Degrees 2, 3, 4, and cross XY
    • Linear
  • JEDi uses subspace analysis to assess the similarity of essential vector spaces defined by each dynamical method:
    • Inter-Model within each type of PCA
    • Inter-Type when subsets yield subspaces with matching dimensions
  • JEDi computes the Free Energy of a trajectory from two PCs (normed projections) so that a FE surface can be constructed.
  • JEDi produces PDB frames that capture the PCA modes and script files for viewing those frames in PyMol(TM) as movies:
    • Individual modes
    • The superposition of the Top Essential Modes
  • For each JEDi run, a comprehensive log file is generated with time stamp recoding the parameters and key results of each analysis

Thank you for using JED and JEDi software:

  • Please report bugs by submitting a new issue tagged with BUG:

    • Be sure to provide enough data to reproduce the error
    • Include JED/JEDi input files, JED/JEDi errors, and associated 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:

  • Check out this link for a demonstration video for using JEDi:

Charles David: [email protected]

Last Software Update: December, 2020
  • New Java Docs
  • New executable JAR files

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