EnGens Usage

Usage

There are a two different use-cases for the EnGens pipeline

1. Static use-case (crystal structures or modelled structures)

2. Dynamic use-case (MD trajectories)

Static use-case

Static use-case:

• Run static workflow of EnGens
• Extract features from the PDB files
  • Step 1 - load the structure and trajectory
  • Step 2 - select different featurizations
  • Step 3 - evaluate the featurizations
  • Not an option for crystal structure input!!
  • Step 4 - pick the featurization
  • Step 5 - save the results as input for Workflow2 - dimensionality reduction

Dynamic use-case

Dynamic use-case:

• Workflow 1 - extract features from the trajectory
  • Step 1 - load the structure and trajectory
  • Step 2 - select different featurizations
  • Step 3 - evaluate the featurizations
  • Step 4 - pick the featurization
  • Step 5 - save the results as input for Workflow2 - dimensionality reduction
• Workflow 2 - reduce the dimensionality of the featurized trajectory
  • Step 0 - Load the results from Workflow1
  • Step 1 - Choose the method for dimensionality reduction and apply it
  • Step 2 - inspect the results visually
  • Step 3 - save results for Workflow3 and clustering
• Workflow 3 - cluster the trajectory
  • Step 0 - Load data from Workflow2
  • Step 1 - choose the clustering method
  • Step 2 - run the clustering with different parameters
  • Step 3 - optionally pick a subset of clusters with the heighest weight
  • Step 4 - extract conformations for the ensemble
  • Step 5 - save results for analysis
• Workflow 4 - analyze the results
  • Cluster plots
  • View multiple structures per cluster
  • Trajectory movie
  • Additional info per cluster - distance between two residues
  • Additional info per cluster - RMSD to a frame
  • Additional info per cluster - RMSD to another structure (given a PDB file)
  • Additional info per cluster - component from dimensionality reduction