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Contents
 
Introduction
Help Videos
Reference Guide
Getting Started
Protein Structure
 Convert to ICM Object
 Pocket Display
 Crystallographic Analysis
 Protein Superposition
 Protein Structure Analysis
 3D Predict
 3D Similarity
 Scan Pockets
Molecular Graphics
Slides & ActiveICM
Sequences & Alignments
Protein Modeling
Cheminformatics
Learn and Predict
Docking
Virtual Screening
Molecular Dynamics
MolScreen
3D Ligand Editor
Tables and Plots
Local Databases
ICM-Scarab
KNIME
Tutorials
FAQs
 
Index
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5.8 Scan Pockets by 3D Pharmacophore
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This feature is described in this publication by Max Totrov BMC Bioinformatics 2011.

This binding site comparison algorithm utilizes optimal superposition of continuous pharmacophoric property distributions, this method offers high sensitivity in identifying both distantly homologous and convergent binding sites, demonstrating reliable superposition quality across multiple examples and enabling the effective clustering of ligand binding pockets in PDB.

To run:

  • First read in your query protein structure.
  • Convert your PDB structure into an ICM object.
  • Go to Tools/Scan Pockets
  • Either select the ligand or make a selection of the pocket and choose the tab "Pocket Atoms"
  • ICM comes with a small compact database to search (pcktmSites.icb.gz) but for a full search use the link in the dialog window to download the full database to search pcktmSitesFull.molt

A results table called SiteHits will be displayed ranking the top scoring PDBs that match the query pocket. The lower the Score value the better the match. Double click on the row and it will superimpose the matched structure onto the query.


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