Active Site Classification
Last update: 8/10/2010
Author: Marc Röttig

ASC documentation

Submitting a job to ASC

  • Adjust the number of classes for your classification task
  • Upload a PDB file
  • Enter substrates within PDB that lie in the active site
    The format is (chain-name,residue-number,residue-name). Multiple substrates can be separated by whitespaces.

  • Optional: If no substrate is co-crystallized with the enzyme you can give position vectors of points lying in the active site.
  • Give a distance cutoff to determine how far away the residues may be away from the substrate
  • Upload a FASTA file for each class and supply a classname

Extracting active site residues only (without any classification)

  • Like above, but simply use only one class

Retrieving a finished job from ASC

  • Enter the job number in the field in the upper right corner and click Analyze to
    view the results or Classify to use the model to classify new sequences

Interpreting ASC results

  • When retrieving a finished ASC job you get a result page as depicted below.
  • On top (ASC results) several statistics of your job are given.
    These are :
    • the JobId
    • the number of classes your classification task has
    • your specified class names
    • the number of samples in each class
    • the specified cutoff distance
    • the performance (F-Measure) during the nested cross validation
  • On the bottom (Signature Overview) the extracted signatures from each sequence are given.
    • the first rows give the ranks of each signature position that were calculated by ASC.
      Each row gives the ranks of one pairwise discrimination task.
    • the next rows contain the signatures
    • the first column gives the names of the training sequences
    • you can color the amino acids according to their descriptor values using the "Color by descriptor" dropdown menu

Interpreting ASC results: Combined view on structure and function

  • When clicking on the button "Show active site" a JMol applet will become visible
  • The JMol applet give as view on the active site of the template structure.
  • When clicking on any signature column the residue corresponding to that position in
    the template structure (JMol view) gets highlighted. In the example below the top ranking residue is selected.
  • Hovering with the mouse over the signature columns will display information about the
    current column (i.e. signature index and PDB residue coresponding to that signature position).
  • The structure within the JMol applet can be rotated and zoomed.

Make predictions using your ASC model

  • Enter your JobId into the field on the top right corner.
  • Click on Predict
  • Upload your FASTA file with sequences to predict
  • You will receive a report page similar to Interpreting ASC results
  • The leading numbers give the predicted class labels
  • Details about the trained ASC are given on top of the page for reference