ICM User's Guide: Sample Peptide

Feb 13 2026 Feedback.

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Contents


Introduction
Help Videos
Reference Guide
Getting Started
Protein Structure
Molecular Graphics
Slides & ActiveICM
Sequences & Alignments
Protein Modeling
Homology Modeling
Renumber
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
Molecular Dynamics
MolScreen
3D Ligand Editor
Tables and Plots
Local Databases
ICM-Scarab
KNIME
Tutorials
FAQs

Index

ICM User's Guide
9.20 Sample Peptide

To model a peptide using the ICM Biased Probability Monte Carlo method:

MolMechanics/Sample Peptide
Enter a name for the simulation.
Enter the one letter amino acid code for the peptide.
Choose whether the peptide is cyclic or not.
Determine the state of the N-terminus and C-terminus.
Add a value for the effort. This represents the length of the simulation - values between 1 and 10 will give a thorough sampling. A larger effort value will be needed for longer peptides.
When the simulation is finished a stack of conformations will be displayed in the ICM workspace.

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