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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
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Docking
Virtual Screening
Molecular Dynamics
MolScreen
3D Ligand Editor
Tables and Plots
Local Databases
ICM-Scarab
KNIME
Tutorials
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Index
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9.5 Loop Preferred Residues
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For a given segment of polypeptide chain ("loop") this method scans the PDB database for segments that have similar conformations (within "vicinity") and calculates relative frequencies of residues at each position. Thus you can find out if certain residues might be preferred in some positions, for instance in beta-turns depending on the type a glycine or a proline might be preferred.


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