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Introduction
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Reference Guide
Getting Started
Protein Structure
Molecular Graphics
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Sequences & Alignments
Protein Modeling
 Homology Modeling
 Loop Modeling
 Design Loop
 Graft Loop
 Loop Preferred Residues
 Find PDB Loop Segment
 Regul
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 Mutation - Protein Binding
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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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