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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
9.3 Design Loop
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Available in the following product(s): Homology

To design a loop between a gap in your protein structure use the MolMechanics/Design Loop option. This option will search for loops in the PDB which have a similar gap distance and geometry and output energetically favorable solutions detailing which PDB the loop was taken from. If you already have a loop and want to sample it use the loop model option.

Step 1: Read in the PDB structure.

Step 2: Convert the PDB structure to an ICM object.

Step 3: Locate the gap where you want to design the loop. Gaps are represented by dashed lines when the structure is displayed in ribbon format.

Step 4: Select the N-terminal residue and copy the green selection to orange.

Step 5: Select the C-terminal residue.

Step 6: Choose MolMechanics/Design Loop menu option.

Step 7: A table called LOOPS with the loop results will be displayed. Double click on the table to load the loop or use the stack display options in the ICM workspace. The loops are ranked by energy in the table and the column names refer to:
  • i rank in stack
  • ener Energy kcal/mol
  • rmsd the distance (either Cartesian or angular RMSD) between the current conformation
  • PDBloop PDB code and residues numbers that the loop was designed on
  • Resolution Resolution of PDB template listed in PDBloop.

Step 8: Note the PDB upon which the loop design is based is listed in the table.


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