Feb 16 2024 Feedback.
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
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
PrevICM User's Guide
5.7 3D Similarity PDB Search
Next

This option will search the PDB for similar structure/folds to the query protein. You can search by the whole protein, a selection or non-contiguous selection (e.g. ligand binding pocket).

  • First read in your query protein structure.
  • Next select the whole protein, a selection or non-contiguous s election (e.g. ligand binding pocket).
  • You can then right click and choose "3D protein similarity search" or select it in the Tools menu.
  • A dialog box will be displayed and there is an option to update PDB index. First update your index - it might take a few minutes.
  • Then select the rmsd search threshold - ICM will not report any hits higher than the threshold
  • Click OK to run the search.
  • A table will then be displayed reporting the hits ranked by rmsd.
  • Double click to load the structure and superimpose it onto your query protein.


Prev
Identify Ligand Pockets
Home
Up
Next
Convert to ICM Object

Copyright© 1989-2020, Molsoft,LLC - All Rights Reserved.
This document contains proprietary and confidential information of Molsoft, LLC.
The content of this document may not be disclosed to third parties, copied or duplicated in any form,
in whole or in part, without the prior written permission from Molsoft, LLC.