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:

https://github.com/charlesdavid/JED

https://github.com/charlesdavid/JEDi

• 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:

  • https://www.youtube.com/watch?v=3I08oGQShwg

Charles David: charles.david@plantandfood.co.nz

Last Software Update: December, 2020

• New Java Docs
• New executable JAR files