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Contents
 
Introduction
Help Videos
Reference Guide
Getting Started
Protein Structure
Molecular Graphics
Slides & ActiveICM
Sequences & Alignments
Protein Modeling
 Homology Modeling
 Loop Modeling
 Design Loop
 Graft Loop
 Loop Preferred Residues
 Find PDB Loop Segment
 Regul
 Refine SC
 Make Disulfide Bond
 Make a Mutation
 Modify Amino Acid
 Mutation - Protein Binding
 Mutation - Protein Stability
 Protein Peptide
 Protein Ligand
 Disulfide Bond
 Sculpting
 Sample Protein
 Sample Peptide
 Molecular Mechanics
Cheminformatics
Learn and Predict
Docking
Virtual Screening
MolScreen
3D Ligand Editor
Tables and Plots
Local Databases
ICM-Scarab
KNIME
Tutorials
FAQs
 
Index
PrevICM User's Guide
9.15 Effect of Mutation on Protein Ligand Binding
Next

To predict the effect of mutation on Protein Ligand Binding:

  • Read in your PDB structure. The ligand and receptor have to be in the same object.
  • Select the residue you wish to mutate
  • Go to MolMechanics/Try Mutation/Protein Ligand Binding
  • Select the ligand in the drop down menu.
  • Select the amino acids you would like to try.
  • Scan Pocket Surface This option will try a single residue side-chain mutation at each position in the protein that is in contact with the receptor.
  • Keep All Chains will maintain the full PDB file in the results table.

Results

  • A table will be displayed with the calculated ddG(kcal/mol) for each mutation selected.


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